diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 8144654..7bb9739 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -8,7 +8,8 @@ on:
branches:
- master
schedule:
- - cron: '0 0 1 * *'
+ - cron: '0 6 * * *'
+ workflow_dispatch:
jobs:
test:
@@ -17,25 +18,54 @@ jobs:
steps:
- name: Checkout
- uses: actions/checkout@v4
+ uses: actions/checkout@v7
- name: Setup Micromamba
- uses: mamba-org/setup-micromamba@v1
+ uses: mamba-org/setup-micromamba@v3
with:
micromamba-version: '1.5.10-0' # any version from https://github.com/mamba-org/micromamba-releases
post-cleanup: 'all'
- # Pinned, not 'latest': main.nf needs `nextflow.preview.topic`, which 25.x removed once
- # topic channels became stable. 24.10.5 is what the cluster runs, so CI matches production.
- - name: Setup Nextflow
- uses: nf-core/setup-nextflow@v2
+ - name: Setup Nextflow (minimum supported version)
+ uses: nf-core/setup-nextflow@v3
+ with:
+ version: '25.04.0'
+
+ - name: Install nf-test
+ uses: nf-core/setup-nf-test@v2
+ with:
+ version: 0.9.5
+
+ - name: Run Tests
+ run: nf-test test --verbose
+
+ test-latest-nextflow:
+ # Runs on a schedule (and manually), not on every push/PR: this catches a future
+ # Nextflow release breaking us, without blocking normal PRs on an upstream change
+ # unrelated to them.
+ if: github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'
+ runs-on: ubuntu-latest
+ timeout-minutes: 60
+
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v7
+
+ - name: Setup Micromamba
+ uses: mamba-org/setup-micromamba@v3
+ with:
+ micromamba-version: '1.5.10-0' # any version from https://github.com/mamba-org/micromamba-releases
+ post-cleanup: 'all'
+
+ - name: Setup Nextflow (latest)
+ uses: nf-core/setup-nextflow@v3
with:
version: "24.10.5"
# Pinned: nf-test serialises the workflow.trace map in a version-dependent key order, so
# every tests/*.snap must be generated with the same version this installs.
- name: Install nf-test
- uses: nf-core/setup-nf-test@v1
+ uses: nf-core/setup-nf-test@v2
with:
version: 0.9.5
diff --git a/.gitignore b/.gitignore
index cab55c5..6b3b7fc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,6 @@
.nextflow*
work
-output
+*output/
ngs-agg_revision.yaml
**/.DS_Store
.vscode/
diff --git a/BENCHMARK_RESULTS.md b/BENCHMARK_RESULTS.md
new file mode 100644
index 0000000..21446e8
--- /dev/null
+++ b/BENCHMARK_RESULTS.md
@@ -0,0 +1,40 @@
+# Benchmark results: bamadap + fgumi zipper + picodup vs the current pipeline
+
+Performance changes in branch: `bamslice_zip`
+
+**Bottom line**: ~2.4x faster end-to-end on a clean dedicated node (16m/6m45s), with indistinguishable output. Correctness verified in depth (§2);
+
+## 1. What changed, and the measured impact
+
+| Change | Impact |
+| --- | --- |
+| `fastp`+`bwa`+Picard-dedup pipeline → `bamadap` + `fgumi zipper` + `picodup`, fused into single-pipe `trimAndAlign` + streamed `mergeAndPicodup` | End-to-end: **16m → 6m45s (~2.4x)** |
+| Dedup: Picard `MarkDuplicates` → `picodup`, streamed straight off `samtools merge` (no intermediate merged BAM) | **2m02s → 27s (~4.6x)**, peak RSS 8.5GB → <1GB |
+| Fixed a real `bwameth.py` bug (naive interleave-detection failed on `bamadap`'s `read/1`,`read/2` mate names, silently mis-converting bisulfite reads); fixed via `bamadap --no-mate-suffix` rather than a downstream patch | Removes a 3x slowdown *and* a silent correctness bug in the align stage |
+| `convert_methylkit_to_bed`: single-threaded `gawk` → `mawk` under `parallel --pipepart` | **7m53s → 35s (~14x)** — biggest single bottleneck in either pipeline; benefits `master` too |
+| `tasmanian` 1.x (single-threaded, capped at 2M reads, errored on some real reads) → `tasmanian-mismatch` 2.x (parallel, full library) | **3m42s → 17.5s (~13x), on more data** |
+| `fastqc` → `falco` | 57.8s → 30.8s (~2x) |
+| Fixed `gc_bias` (silently broken: `CollectGcBiasMetrics` requires an `Rscript` on PATH even when no chart is produced; `picard-slim` excludes R) | No-op `Rscript` shim; restores a previously-silent-failing QC step |
+| Right-sized cpu reservations for QC steps that don't read `task.cpus` (new `single_threaded_qc` label, fixed at 2 cpus instead of scaling with `--max_cpus`) | Frees queue slots on shared executors; no effect on single-task time |
+| Kept `bwameth --read-group` (populated from the uBAM's first `@RG`) instead of dropping it as originally planned; `zipper` still fixes the per-read `RG:Z:` tag | Avoids `picodup` mislabeling every metric row "Unknown Library" |
+| Fixed `bamadap`'s EL8 build (glibc-2.34-only symbols, `target-cpu=native` SIGILL'd on other CPUs) | Portability now solved at deploy time, not build time: Capistrano (`capistrano-rust-buildcache`) compiles a `-C target-cpu=native` binary per distinct machine type on first run and caches it, rather than shipping one generic binary |
+
+Chunk-size sweep on the real SGE cluster (18/37/55/90MB): smaller chunks buy wall-clock speed at
+the cost of more aggregate CPU-hours (7m14s/7.1 CPU-h at 18MB vs. 10m18s/4.4 CPU-h at 90MB); no
+change made to the 37MB default — it's a reasonable middle ground, not a correctness question.
+
+## 2. Correctness (final `.md.bam`, same test uBAM)
+
+| | Baseline | New | Δ |
+| --- | --- | --- | --- |
+| Total reads | 10,017,473 | 10,017,757 | +0.003% |
+| Duplicates | 1,362,823 | 1,362,959 | +0.01% |
+| PERCENT_DUPLICATION | 0.136415 | 0.136426 | matches to 4th decimal |
+| CpG methylation (Pearson r) | — | **0.999998** | 5 sites (0.0001%) differ by >1pp |
+
+Residual differences trace to expected causes (`bamadap` vs `fastp` trimming, corrected
+per-read `RG` moving optical-duplicate grouping, each dedup tool's own library-size extrapolation
+formula) — no read loss, no regression. `ngs-aggregate_results` compatibility for
+`tasmanian-mismatch` 2.x's new output format was verified against the real deployed parser
+(PR #932, merged and deployed 2026-09-07) and an end-to-end real (non-stubbed) aggregation run
+succeeded.
diff --git a/README.md b/README.md
index 526d62c..441c07d 100644
--- a/README.md
+++ b/README.md
@@ -206,9 +206,6 @@ nf-test test --updateSnapshot
```
## Upgrade
-Nextflow dropped upstream support for v24 and older in July 2026, but this pipeline still targets
-24.10.x -- that is what CI pins and what the reference runs use -- so *main.nf* ships with
-`nextflow.preview.topic = true` as its top line.
-
-Nextflow 25.x made topic channels stable and removed that directive. To run on 25.x or newer,
-comment out or delete that top line of *main.nf*.
+This pipeline requires Nextflow >=25.04, where topic channels (used throughout for
+version reporting) are a stable feature rather than a preview one. `main.nf` checks
+this at startup and fails immediately with a clear message on older versions.
diff --git a/conf/base.config b/conf/base.config
index 468ec99..957899a 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -23,6 +23,14 @@ process {
cpus = { params.max_cpus ?: 8 }
}
+ withLabel: dedup {
+ // Deliberately not capped by params.max_cpus: this label exists so the dedup stage
+ // can be tuned independently of the trim/align concurrency (see BENCHMARK_PLAN.md phase 6).
+ // Still capped to whatever the machine actually has, so it doesn't request more cpus
+ // than any executor can ever grant (e.g. GitHub Actions' 4-core runners).
+ cpus = { Math.min(16, Runtime.runtime.availableProcessors()) }
+ }
+
withLabel: low_cpu {
cpus = 2
memory = { params.max_memory ?: 16.GB }
@@ -38,6 +46,14 @@ process {
memory = { params.max_memory ?: 8.GB }
}
+ withLabel: single_threaded_qc {
+ // For fastqc (falco), gc_bias, insert_size_metrics, picard_metrics, idx_stats:
+ // none of them read task.cpus, so scaling with params.max_cpus like medium_cpu
+ // would only reserve idle cpu slots, starving other queued tasks on the local
+ // executor for no speed benefit.
+ cpus = 2
+ }
+
executor = 'local' // 'sge'. 'slurm', etc...
diff --git a/conf/references.config b/conf/references.config
index 8ae764b..02618e1 100644
--- a/conf/references.config
+++ b/conf/references.config
@@ -4,12 +4,13 @@
// whole-reference curve alone. See "GC bias curves" in the README for the directory's contents.
params {
genomes = [
- 'T2T_chm13v2.0+bs_controls': [
- bwa_index: "/bioinfo/ref/T2T_chm13v2.0+bs_controls/bwameth/T2T_chm13v2.0+bs_controls.fa",
- genome_fa: "/bioinfo/ref/T2T_chm13v2.0+bs_controls/bwameth/T2T_chm13v2.0+bs_controls.fa",
- genome_fai: "/bioinfo/ref/T2T_chm13v2.0+bs_controls/bwameth/T2T_chm13v2.0+bs_controls.fa.fai",
- gc_groups_dir: "/bioinfo/ref/T2T_chm13v2.0+bs_controls/gc_groups",
- target_bed: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/folded_windows/T2T_chm13v2.0+meth_controls_hairpins.s18w200nogt.bed"
+ 'T2T_chm13v2.0+meth_controls': [
+ bwa_index: "/bioinfo/ref/t2t_chm13v2+meth_controls/bwameth_index/T2T_chm13v2.0+bs_controls.fa",
+ genome_fa: "/bioinfo/ref/t2t_chm13v2+meth_controls/bwameth_index/T2T_chm13v2.0+bs_controls.fa",
+ genome_fai: "/bioinfo/ref/t2t_chm13v2+meth_controls/bwameth_index/T2T_chm13v2.0+bs_controls.fa.fai",
+ genome_dict:"/bioinfo/ref/t2t_chm13v2+meth_controls/bwameth_index/T2T_chm13v2.0+bs_controls.fa.dict",
+ gc_groups_dir: "/bioinfo/ref/t2t_chm13v2+meth_controls/gc_groups",
+ target_bed: "/bioinfo/ref/t2t_chm13v2+meth_controls/folded_windows/T2T_chm13v2.0+meth_controls_hairpins.s18w200nogt.bed",
],
'grcm39+meth_controls': [
bwa_index: "/bioinfo/ref/grcm39+meth_controls/bwameth/grcm39+meth_controls.fa",
@@ -51,6 +52,7 @@ params {
bwa_index: "${projectDir}/tests/fixtures/reference_files/reference.fa",
genome_fa: "${projectDir}/tests/fixtures/reference_files/reference.fa",
genome_fai: "${projectDir}/tests/fixtures/reference_files/reference.fa.fai",
+ genome_dict: "${projectDir}/tests/fixtures/reference_files/reference.dict",
gc_groups_dir: "${projectDir}/tests/fixtures/reference_files/gc_groups",
target_bed: "${projectDir}/tests/fixtures/target_bed/emseq_test_regions.bed"
],
@@ -60,6 +62,7 @@ params {
bwa_index: "${projectDir}/tests/fixtures/reference_files/reference.fa",
genome_fa: "${projectDir}/tests/fixtures/reference_files/reference.fa",
genome_fai: "${projectDir}/tests/fixtures/reference_files/reference.fa.fai",
+ genome_dict: "${projectDir}/tests/fixtures/reference_files/reference.dict",
target_bed: "${projectDir}/tests/fixtures/target_bed/emseq_test_regions.bed"
]
]
diff --git a/conf/test.config b/conf/test.config
index 89066ec..2eb201e 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -11,20 +11,27 @@
*/
process{
- executor = 'local'
+ executor = 'local'
}
params {
- config_profile_name = 'Test profile'
- config_profile_description = 'Minimal test dataset to check pipeline function'
-
- // Limit resources so that this can run on GitHub Actions
- max_cpus = 2
- max_memory = '6.GB'
- max_time = '6.h'
-
- outputDir = "test_output"
- }
+ config_profile_name = 'Test profile'
+ config_profile_description = 'Minimal test dataset to check pipeline function'
+
+ // Limit resources so that this can run on GitHub Actions
+ max_cpus = 2
+ max_memory = '6.GB'
+ max_time = '6.h'
+
+ outputDir = "test_output"
+
+ // Not yet on bioconda. nf-test's pipeline tests run trimAndAlign/mergeAndPicodup under
+ // -stub-run (see their stub: blocks), so CI never actually invokes these paths -- they
+ // only matter for a manual, non-stub `nextflow run main.nf -profile test`.
+ bamadap_bin = '/appdev/langhorst/src/bamadap/target-el8/release/bamadap'
+ picodup_bin = '/appdev/langhorst/src/picodup/target-el8/release/picodup'
+ bamslice_bin = '/appdev/langhorst/src/bamslice/target-el8/release/bamslice'
+}
- trace.overwrite = true
+trace.overwrite = true
diff --git a/lib/notifications.nf b/lib/notifications.nf
index 06f4323..56803e2 100644
--- a/lib/notifications.nf
+++ b/lib/notifications.nf
@@ -1,4 +1,5 @@
-def notificationHtml(String status) {
+// `wf` is the live WorkflowMetadata object captured by registerEmailNotifications
+def notificationHtml(String status, String pipelineName, wf) {
def isSuccess = status == 'SUCCESS'
def bannerBg = isSuccess ? '#dff0d8' : '#f2dede'
def bannerBorder = isSuccess ? '#d6e9c6' : '#ebccd1'
@@ -6,35 +7,35 @@ def notificationHtml(String status) {
def bannerMsg = isSuccess ? 'Execution completed successfully!' : 'Execution failed!'
def rows = []
- rows << ['Pipeline', params.workflow ?: '-']
- rows << ['Run name', workflow.runName]
- rows << ['Launch time', workflow.start]
- if (workflow.complete) {
- rows << ['Ending time', "${workflow.complete} (duration: ${workflow.duration})"]
+ rows << ['Pipeline', pipelineName ?: '-']
+ rows << ['Run name', wf.runName]
+ rows << ['Launch time', wf.start]
+ if (wf.complete) {
+ rows << ['Ending time', "${wf.complete} (duration: ${wf.duration})"]
}
def stats = null
- try { stats = workflow.stats } catch (Exception e) { }
+ try { stats = wf.stats } catch (Exception e) { }
if (stats) {
rows << ['Tasks stats', "Succeeded: ${stats.succeededCount} Cached: ${stats.cachedCount} Ignored: ${stats.ignoredCount} Failed: ${stats.failedCount}"]
}
- rows << ['Launch directory', workflow.launchDir]
- rows << ['Work directory', workflow.workDir]
- rows << ['Project directory', workflow.projectDir]
- rows << ['Script name', workflow.scriptName]
- rows << ['Script ID', workflow.scriptId]
- rows << ['Workflow session', workflow.sessionId]
- if (workflow.profile) rows << ['Workflow profile', workflow.profile]
- rows << ['Nextflow version', "${workflow.nextflow.version}, build ${workflow.nextflow.build}"]
+ rows << ['Launch directory', wf.launchDir]
+ rows << ['Work directory', wf.workDir]
+ rows << ['Project directory', wf.projectDir]
+ rows << ['Script name', wf.scriptName]
+ rows << ['Script ID', wf.scriptId]
+ rows << ['Workflow session', wf.sessionId]
+ if (wf.profile) rows << ['Workflow profile', wf.profile]
+ rows << ['Nextflow version', "${wf.nextflow.version}, build ${wf.nextflow.build}"]
def rowsHtml = rows.collect { pair ->
" | ${pair[0]} | ${pair[1] ?: '-'} |
"
}.join('\n')
def errorBlock = ''
- if (!isSuccess && workflow.errorMessage) {
+ if (!isSuccess && wf.errorMessage) {
errorBlock = """
Error:
- ${workflow.errorMessage}
+ ${wf.errorMessage}
"""
}
@@ -44,14 +45,14 @@ def notificationHtml(String status) {
Workflow ${isSuccess ? 'completion' : 'failure'} notification
- Run Name: ${workflow.runName}
+ Run Name: ${wf.runName}
${bannerMsg}
${errorBlock}
The command used to launch the workflow was as follows:
- ${workflow.commandLine}
+ ${wf.commandLine}
Execution summary
@@ -65,15 +66,20 @@ ${rowsHtml}
def registerEmailNotifications() {
if (params.dry_run || workflow.stubRun) return
+ // workflow.onError/onComplete run detached from this binding, so bare `params.*`/`workflow.*`
+ // throw NPEs there; capture into locals below so closure capture picks them up instead.
+ def wf = workflow
+ def recipients = [params.email, params.admin_email].findAll { it }.join(',')
+ def pipelineName = params.workflow ?: 'unknown'
+
def notified = false
workflow.onError {
- def recipients = [params.email, params.admin_email].findAll { it }.join(',')
if (!recipients) return
sendMail(
to: recipients,
- subject: "[Pipeline FAILED] ${params.workflow ?: 'unknown'} - ${workflow.runName}",
- body: notificationHtml('FAILED'),
+ subject: "[Pipeline FAILED] ${pipelineName} - ${wf.runName}",
+ body: notificationHtml('FAILED', pipelineName, wf),
type: 'text/html'
)
notified = true
@@ -81,13 +87,12 @@ def registerEmailNotifications() {
workflow.onComplete {
if (notified) return
- def recipients = [params.email, params.admin_email].findAll { it }.join(',')
if (!recipients) return
- def status = workflow.success ? 'SUCCESS' : 'FAILED'
+ def status = wf.success ? 'SUCCESS' : 'FAILED'
sendMail(
to: recipients,
- subject: "[Pipeline ${status}] ${params.workflow} - ${workflow.runName}",
- body: notificationHtml(status),
+ subject: "[Pipeline ${status}] ${pipelineName} - ${wf.runName}",
+ body: notificationHtml(status, pipelineName, wf),
type: 'text/html'
)
}
diff --git a/main.nf b/main.nf
index 048f51f..0244fed 100644
--- a/main.nf
+++ b/main.nf
@@ -1,12 +1,14 @@
-nextflow.preview.topic = true
+// Minimum version: topic channels are stable here, preview (and unsupported) before it.
+if (!nextflow.version.matches('>=25.04')) {
+ error "This pipeline requires Nextflow >=25.04. Found: ${nextflow.version}."
+}
include { registerEmailNotifications } from './lib/notifications.nf'
include { createVersionsFile } from './lib/versions.nf'
include { format_ngs_agg_opts } from './modules/aggregate_results'
-include { fastp } from './modules/fastp'
include { mergeFastpJson } from './modules/merge_fastp_json'
-include { alignReads } from './modules/align_reads'
-include { mergeAndMarkDuplicates } from './modules/merge_and_mark_duplicates'
+include { trimAndAlign } from './modules/trim_and_align'
+include { mergeAndPicodup } from './modules/merge_and_picodup'
include { methylDackel_mbias } from './modules/methyldackel_mbias'
include { methylDackel_extract } from './modules/methyldackel_extract'
include { extract_cytosine_report } from './modules/extract_cytosine_report'
@@ -55,6 +57,7 @@ workflow {
def reference_list = params.genomes[params.genome]
genome_fa = channel.value(reference_list.genome_fa)
genome_fai = channel.value(reference_list.genome_fai)
+ genome_dict = channel.value(reference_list.genome_dict)
// Validate reference indices exist before running
def ref = reference_list.bwa_index
@@ -64,6 +67,9 @@ workflow {
if (!file("${reference_list.genome_fa}.fai").exists()) {
exit 1, "Fasta index (.fai) not found for ${reference_list.genome_fa}. Run: samtools faidx ${reference_list.genome_fa}"
}
+ if (!reference_list.genome_dict || !file(reference_list.genome_dict).exists()) {
+ exit 1, "Sequence dictionary not found for ${reference_list.genome_fa}. Run: samtools dict ${reference_list.genome_fa} -o [.dict"
+ }
passed_bams = bams.filter { _library, bam -> checkFileSize(bam) }
failed_bams = bams.filter { _library, bam -> !checkFileSize(bam) }
@@ -100,23 +106,18 @@ workflow {
}
}
- fastp( passed_bams.combine(bam_chunks, by:0), adapter_fasta )
- mergeFastpJson( fastp.out.fastp_json.groupTuple() )
+ trimAndAlign(
+ passed_bams.combine(bam_chunks, by:0),
+ adapter_fasta,
+ reference_list.bwa_index,
+ genome_fa,
+ genome_fai,
+ genome_dict
+ )
+ mergeFastpJson( trimAndAlign.out.fastp_json.groupTuple() )
- fastq_chunks = fastp.out.trimmed_fastq.map { library, chunk_name, fq_files ->
- def fq_list = fq_files instanceof List ? fq_files : [fq_files]
- if (params.single_end) {
- tuple(library, chunk_name, fq_list[0])
- }
- else {
- def r1 = fq_list.find { fq -> fq.name.contains('.1.trimmed.fastq') }
- def r2 = fq_list.find { fq -> fq.name.contains('.2.trimmed.fastq') }
- tuple(library, chunk_name, [r1, r2])
- }
- }
- alignReads( passed_bams.combine(fastq_chunks, by:0), reference_list.bwa_index )
- mergeAndMarkDuplicates( alignReads.out.bam_files.groupTuple() )
- md_bams = mergeAndMarkDuplicates.out.md_bams
+ mergeAndPicodup( trimAndAlign.out.bam_files.groupTuple() )
+ md_bams = mergeAndPicodup.out.md_bams
///////// Methylation Calling //////////
methylDackel_extract( md_bams, genome_fa, genome_fai )
@@ -158,18 +159,18 @@ workflow {
fastqc( md_bams )
picard_metrics( md_bams, genome_fa, genome_fai )
tasmanian( md_bams, genome_fa, genome_fai )
- combine_nonconverted_counts( alignReads.out.nonconverted_counts.groupTuple() )
+ combine_nonconverted_counts( trimAndAlign.out.nonconverted_counts.groupTuple() )
find_switchback_reads( md_bams, genome_fa )
//////// Collect files for internal summaries //////////
agg_opts = [
- ['--bam', mergeAndMarkDuplicates.out.md_bams.map{ row -> tuple(row[0], row[1]) }],
- ['--bai', mergeAndMarkDuplicates.out.md_bams.map{ row -> tuple(row[0], row[2]) }],
+ ['--bam', mergeAndPicodup.out.md_bams.map{ row -> tuple(row[0], row[1]) }],
+ ['--bai', mergeAndPicodup.out.md_bams.map{ row -> tuple(row[0], row[2]) }],
['--metadata_bam_file', bams],
['--fastp', mergeFastpJson.out.merged_json],
['--aln', picard_metrics.out.for_agg ],
['--gc', gc_bias_curves.out.for_agg ],
- ['--dup', mergeAndMarkDuplicates.out.log],
+ ['--dup', mergeAndPicodup.out.log],
['--idx_stats', idx_stats.out.for_agg],
['--flagstat', flagstats.out.for_agg],
['--fastqc', fastqc.out.for_agg],
diff --git a/modules/align_reads.nf b/modules/align_reads.nf
deleted file mode 100644
index bfa90e6..0000000
--- a/modules/align_reads.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-process alignReads {
- label 'high_cpu'
- tag { library }
- conda "conda-forge::python=3.10 bioconda::bwameth=0.2.7 bioconda::mark-nonconverted-reads=1.2 bioconda::samtools=1.22"
- publishDir "${params.outputDir}/bwameth_align", mode: 'symlink'
-
- input:
- tuple val(library), path(bam), val(chunk_name), path(reads)
- val(genome_fa)
-
- output:
- tuple val(library), path("${chunk_name}.aln.bam"), path("${chunk_name}.aln.bam.bai"), emit: bam_files
- tuple val(library), path("${chunk_name}.nonconverted_counts.tsv"), emit: nonconverted_counts
- tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -n 1 | sed \'s/^samtools //\''), topic: versions
- tuple val("${task.process}"), val('bwameth'), eval('bwameth.py --version | sed \'s/^bwa-meth.py //\''), topic: versions
- tuple val("${task.process}"), val('python'), eval('python --version | sed \'s/^Python //\''), topic: versions
-
- script:
- def bwameth_input = params.single_end ? "${reads}" : "-p ${reads[0]} ${reads[1]}"
- """
- set +o pipefail
- rg_line=\$(samtools view -H ${bam} | grep "^@RG" | sed 's/\\t/\\\\t/g' | head -n1)
- set -o pipefail
-
- bwameth.py -t ${Math.max(1,(task.cpus*7).intdiv(8))} --read-group "\${rg_line}" --reference ${genome_fa} ${bwameth_input} 2> "${library}.log.bwamem" \
- | mark-nonconverted-reads.py --reference ${genome_fa} 2> "${chunk_name}.nonconverted_counts.tsv" \
- | samtools sort -T ${params.tmp_dir}/samtools_sort_tmp -@ ${Math.max(1,task.cpus.intdiv(8))} \
- -m ${(task.memory.toGiga()*5).intdiv(8)}G --write-index \
- -o "${chunk_name}.aln.bam##idx##${chunk_name}.aln.bam.bai" /dev/stdin
-
- """
-}
diff --git a/modules/convert_methylkit_to_bed.nf b/modules/convert_methylkit_to_bed.nf
index 242b3b6..5db7ac7 100644
--- a/modules/convert_methylkit_to_bed.nf
+++ b/modules/convert_methylkit_to_bed.nf
@@ -1,7 +1,7 @@
process convert_methylkit_to_bed {
- label 'process_single'
+ label 'cpus_8'
tag "${library}"
- conda "conda-forge::pigz=2.8 conda-forge::gawk=5.3.1 conda-forge::sed=4.9"
+ conda "conda-forge::parallel=20250622 bioconda::mawk=1.3.4"
input:
tuple val(library), path(cytosine_report)
@@ -12,31 +12,27 @@ process convert_methylkit_to_bed {
tuple val(library), path("${library}.bed"), emit: methylkit_bed
script:
- // Using cytosine report as a substitute for merging 3 methylkit files.
- // Reports C's with no coverage, so we will filter those out
+ // Using cytosine report as a substitute for merging 3 methylkit files.
+ // Reports C's with no coverage, so we will filter those out.
+ //
+ // Rows are independent, so `parallel --pipepart` seeks into byte ranges of the
+ // file with no copy and runs mawk over each concurrently; `--keep-order` keeps
+ // the output in the sorted order `bedtools intersect -sorted` needs downstream.
"""
+ # A script file, not an inline awk program: `parallel` re-quotes the command it
+ # hands each worker, which mangles braces and \$N as its own syntax.
+ cat <<'AWK' > convert_methylkit.awk
+ BEGIN { OFS = "\t" }
# Input: chromosome, position (1-based), strand, meth_count, unmeth_count, context, trinucleotide
- # Output: chr, start (0-based), end (1-based), context, methylation_freq, strand
- awk '
- BEGIN { OFS = "\t" }
- !( \$4==0 && \$5==0 ){
- chromosome = \$1
- position = \$2
- strand = \$3
- meth_count = \$4
- unmeth_count = \$5
- context = \$6
-
- # Calculate methylation frequency
- total_count = meth_count + unmeth_count
- meth_freq = (total_count > 0) ? (meth_count / total_count * 100) : 0
-
- # Convert to BED format (0-based start, 1-based end)
- start = position - 1
- end = position
-
- print chromosome, start, end, context, meth_freq, strand
- }
- ' ${cytosine_report} > "${library}.bed"
+ !( \$4==0 && \$5==0 ){
+ total_count = \$4 + \$5
+ meth_freq = (total_count > 0) ? (\$4 / total_count * 100) : 0
+ # Output: chr, start (0-based), end (1-based), context, methylation_freq, strand
+ print \$1, \$2 - 1, \$2, \$6, meth_freq, \$3
+ }
+ AWK
+
+ parallel --pipepart --keep-order -j ${task.cpus} -a ${cytosine_report} \\
+ mawk -f convert_methylkit.awk > "${library}.bed"
"""
}
diff --git a/modules/fastp.nf b/modules/fastp.nf
deleted file mode 100644
index 10b0ccf..0000000
--- a/modules/fastp.nf
+++ /dev/null
@@ -1,38 +0,0 @@
-process fastp {
- tag "${library}"
- label 'low_cpu'
- conda "bioconda::samtools=1.21 bioconda::fastp=1.3.6 bioconda::bamslice=0.2.1"
- publishDir "${params.outputDir}/fastp"
-
- input:
- tuple val(library), path(bam), val(start_offset), val(end_offset)
- path(adapter_fasta)
-
- output:
- tuple val(library), val("${library}_${start_offset}_${end_offset}"), path("${library}_${start_offset}_${end_offset}*.trimmed.fastq.gz"), emit: trimmed_fastq
- tuple val(library), val("${library}_${start_offset}_${end_offset}"), path("${library}_${start_offset}_${end_offset}.fastp.json"), emit: fastp_json
- tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -n 1 | sed \'s/^samtools //\''), topic: versions
- tuple val("${task.process}"), val('fastp'), eval('fastp --version 2>&1 | cut -f 2 -d " "'), topic: versions
- tuple val("${task.process}"), val('bamslice'), eval('bamslice --version | cut -f 2 -d " "'), topic: versions
-
- script:
- def chunk = "${library}_${start_offset}_${end_offset}"
- def fastp_args = params.single_end ? "--out1 ${chunk}.1.trimmed.fastq.gz" : "--interleaved_in --out1 ${chunk}.1.trimmed.fastq.gz --out2 ${chunk}.2.trimmed.fastq.gz"
- """
- set +o pipefail
- inst_name=\$(samtools view ${bam} | head -n 1 | cut -d ":" -f 1)
- set -o pipefail
-
- trim_polyg=\$(echo "\${inst_name}" | awk '{if (\$1~/^A0|^NB|^NS|^VH/) {print "--trim_poly_g"} else {print ""}}')
- echo \${trim_polyg} | awk '{ if (length(\$1)>0) { print "2-color instrument: poly-g trim mode on" } }'
-
- bamslice --input ${bam} --start-offset ${start_offset} --end-offset ${end_offset} | \\
- fastp --stdin \\
- -l 2 -Q \${trim_polyg} \\
- --thread 1 \\
- --adapter_fasta ${adapter_fasta} \\
- --overrepresentation_analysis \\
- -j "${chunk}.fastp.json" \\
- ${fastp_args}
- """
-}
diff --git a/modules/fastqc.nf b/modules/fastqc.nf
index f405b9b..c26c07d 100644
--- a/modules/fastqc.nf
+++ b/modules/fastqc.nf
@@ -1,7 +1,7 @@
process fastqc {
- label 'medium_cpu'
+ label 'single_threaded_qc'
tag { library }
- conda "bioconda::fastqc=0.11.8"
+ conda "bioconda::falco=1.0.0 conda-forge::zip=3.0"
publishDir "${params.outputDir}/stats/fastqc"
input:
@@ -10,10 +10,20 @@ process fastqc {
output:
tuple val(library), path('*_fastqc.zip'), emit: for_agg
tuple val(library), path('*_fastqc.html'), emit: html
- tuple val("${task.process}"), val('fastqc'), eval('fastqc --version | cut -f 2 -d " "'), topic: versions
+ tuple val("${task.process}"), val('falco'), eval('falco --version | cut -f 2 -d " "'), topic: versions
script:
+ // falco's own output is flat (fastqc_data.txt, fastqc_report.html, summary.txt;
+ // no per-sample name or archive). Repackage into a _fastqc.zip containing
+ // a _fastqc/ directory — the layout MultiQC's fastqc module and
+ // aggregate_results.nf's `unzip *fastqc.zip` + "fastqc/fastqc_data.txt"
+ // substitution both expect. must be the BAM filename minus ".bam"
+ // (bam.baseName), not the library tag, to match what FastQC itself would name it.
"""
- fastqc -f bam ${bam}
+ falco -f bam ${bam}
+ mkdir ${bam.baseName}_fastqc
+ mv fastqc_data.txt summary.txt ${bam.baseName}_fastqc/
+ zip -rq ${bam.baseName}_fastqc.zip ${bam.baseName}_fastqc
+ mv fastqc_report.html ${bam.baseName}_fastqc.html
"""
}
diff --git a/modules/gc_bias.nf b/modules/gc_bias.nf
index e677006..a1af49d 100644
--- a/modules/gc_bias.nf
+++ b/modules/gc_bias.nf
@@ -3,9 +3,9 @@
// Per-organism curves for a composite genome come from gc_bias_by_contig_group, which streams a
// contig subset of the same BAM against that organism's own reference.
process gc_bias {
+ label 'single_threaded_qc'
tag { library }
- label 'medium_cpu'
- conda "bioconda::picard=3.3.0"
+ conda "bioconda::picard-slim=3.5.0 bioconda::samtools=1.22"
publishDir "${params.outputDir}/stats/gc_bias"
input:
@@ -16,11 +16,22 @@ process gc_bias {
tuple val("${task.process}"), val('picard'), eval('picard CollectGcBiasMetrics --version 2>&1 | cut -f 2 -d ":"'), topic: versions
script:
- // The picard flags here must stay in step with modules/gc_bias_by_contig_group.nf.
+ // CollectGcBiasMetrics checks for an Rscript on PATH even with --CHART /dev/null;
+ // picard-slim excludes R, so shim a no-op Rscript rather than add a real R dependency.
"""
- picard -Xmx${task.memory.toGiga()}g CollectGcBiasMetrics \\
- --IS_BISULFITE_SEQUENCED true --VALIDATION_STRINGENCY SILENT \\
- -I ${bam} -O ${library}.gc_metrics -S ${library}.gc_summary_metrics \\
+ mkdir -p fakebin
+ printf '#!/bin/sh\\nexit 0\\n' > fakebin/Rscript
+ chmod +x fakebin/Rscript
+ export PATH="\$PWD/fakebin:\$PATH"
+
+ samtools view -H ${bam} | grep "^@SQ" \
+ | grep -v "plasmid_puc19\\|phage_lambda\\|phage_Xp12\\|phage_T4\\|EBV\\|chrM" \
+ | awk -F":|\\t" '{print \$3"\\t"0"\\t"\$5}' > include_regions.bed
+
+ samtools view -h -L include_regions.bed ${bam} | \
+ picard -Xmx${task.memory.toGiga()}g CollectGcBiasMetrics \
+ --IS_BISULFITE_SEQUENCED true --VALIDATION_STRINGENCY SILENT \
+ -I /dev/stdin -O ${library}.gc_metrics -S ${library}.gc_summary_metrics \
--CHART /dev/null -R ${picard_reference}
"""
}
diff --git a/modules/idx_stats.nf b/modules/idx_stats.nf
index fcd47c0..fb631c2 100644
--- a/modules/idx_stats.nf
+++ b/modules/idx_stats.nf
@@ -1,5 +1,5 @@
process idx_stats {
- label 'medium_cpu'
+ label 'single_threaded_qc'
tag { library }
conda "bioconda::samtools=1.22"
publishDir "${params.outputDir}/stats/idxstats"
diff --git a/modules/insert_size_metrics.nf b/modules/insert_size_metrics.nf
index c9259d5..93f4407 100644
--- a/modules/insert_size_metrics.nf
+++ b/modules/insert_size_metrics.nf
@@ -1,5 +1,5 @@
process insert_size_metrics {
- label 'medium_cpu'
+ label 'single_threaded_qc'
tag { library }
conda "bioconda::picard=3.3.0 bioconda::samtools=1.22"
publishDir "${params.outputDir}/stats/insert_size"
diff --git a/modules/merge_and_mark_duplicates.nf b/modules/merge_and_mark_duplicates.nf
deleted file mode 100644
index c9f7009..0000000
--- a/modules/merge_and_mark_duplicates.nf
+++ /dev/null
@@ -1,50 +0,0 @@
-process mergeAndMarkDuplicates {
- label 'cpus_8'
- tag { library }
- publishDir "${params.outputDir}/markduped_bams", mode: 'copy', pattern: '*.md.{bam,bai}'
- publishDir "${params.outputDir}/stats/markdups", mode: 'copy', pattern: '*log'
- conda "bioconda::picard=3.3.0 bioconda::samtools=1.22"
- memory {
- try {
- def totalFileSize = bams.collect { bam_file -> bam_file.size() }.sum() / (1024 * 1024 * 1024)
- def calculatedMemory = totalFileSize < 2 ? '32.GB' : totalFileSize < 8 ? '64.GB' : '128.GB'
- return params.max_memory ?: calculatedMemory
- }
- catch (Exception _e) {
- return params.max_memory ?: '64.GB'
- }
-}
-
- input:
- tuple val(library), path(bams), path(bais)
- output:
- tuple val(library), path("${library}.md.bam"), path("${library}.md.bai"), emit: md_bams
- tuple val(library), path('*.markdups_log'), emit: log
- tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -n 1 | sed \'s/^samtools //\''), topic: versions
- tuple val("${task.process}"), val('picard'), eval('picard MarkDuplicates --version 2>&1 | cut -f 2 -d ":"'), topic: versions
-
- script:
- """
- set +o pipefail
- inst_name=\$(samtools view ${bams[0]} | head -n1 | cut -d ":" -f1);
- set -o pipefail
-
- optical_distance=\$(echo \${inst_name} | awk '{if (\$1~/^M0|^NS|^NB/) {print 100} else {print 2500}}')
-
- samtools merge --threads ${task.cpus} ${library}.bam ${bams}
-
- picard -Xmx${task.memory.toGiga().intdiv(2)}g MarkDuplicates \
- --TAGGING_POLICY All \
- --OPTICAL_DUPLICATE_PIXEL_DISTANCE \${optical_distance} \
- --TMP_DIR ${params.tmp_dir} \
- --CREATE_INDEX true \
- --MAX_RECORDS_IN_RAM 5000000 \
- --BARCODE_TAG "RX" \
- --ASSUME_SORT_ORDER coordinate \
- --VALIDATION_STRINGENCY SILENT \
- --ADD_PG_TAG_TO_READS false \
- -I ${library}.bam \
- -O ${library}.md.bam \
- -M ${library}.markdups_log
- """
-}
diff --git a/modules/merge_and_picodup.nf b/modules/merge_and_picodup.nf
new file mode 100644
index 0000000..0890717
--- /dev/null
+++ b/modules/merge_and_picodup.nf
@@ -0,0 +1,53 @@
+process mergeAndPicodup {
+ label 'dedup'
+ tag { library }
+ publishDir "${params.outputDir}/markduped_bams", mode: 'copy', pattern: '*.md.{bam,bai}'
+ publishDir "${params.outputDir}/stats/markdups", mode: 'copy', pattern: '*log'
+ conda "bioconda::samtools=1.22"
+ memory { params.max_memory ?: 16.GB }
+
+ input:
+ tuple val(library), path(bams)
+ output:
+ tuple val(library), path("${library}.md.bam"), path("${library}.md.bai"), emit: md_bams
+ tuple val(library), path('*.markdups_log'), emit: log
+ tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -n 1 | sed \'s/^samtools //\''), topic: versions
+ tuple val("${task.process}"), val('picodup'), eval("${params.picodup_bin} --version | cut -f 2 -d ' '"), topic: versions
+
+ script:
+ def merge_cpus = Math.min(2, task.cpus)
+ def dedup_cpus = Math.max(1, task.cpus - merge_cpus)
+ def optical_distance_line = params.picodup_optical_distance != null
+ ? "optical_distance=${params.picodup_optical_distance}"
+ : 'optical_distance=$(echo ${inst_name} | awk \'{if ($1~/^M0|^NS|^NB/) {print 100} else {print 2500}}\')'
+ """
+ set +o pipefail
+ inst_name=\$(samtools view ${bams[0]} | head -n1 | cut -d ":" -f1)
+ set -o pipefail
+
+ ${optical_distance_line}
+
+ samtools merge --threads ${merge_cpus} -O bam -o - ${bams} \\
+ | ${params.picodup_bin} \\
+ --input /dev/stdin \\
+ --output ${library}.md.bam \\
+ --metrics ${library}.markdups_log \\
+ --threads ${dedup_cpus} \\
+ --optical-model ${params.picodup_optical_model} \\
+ --optical-distance \${optical_distance} \\
+ --tagging-policy All
+
+ samtools index -@ ${task.cpus} ${library}.md.bam ${library}.md.bai
+ """
+
+ stub:
+ // See the matching note in trim_and_align.nf: replays a real picodup run's output for
+ // this library, captured once under tests/fixtures/stub_outputs/, since bamadap/picodup
+ // aren't on bioconda yet and CI has no real binary to run.
+ def fixture_dir = "${workflow.projectDir}/tests/fixtures/stub_outputs/merge_and_picodup"
+ """
+ cp ${fixture_dir}/${library}.md.bam .
+ cp ${fixture_dir}/${library}.md.bai .
+ cp ${fixture_dir}/${library}.markdups_log .
+ """
+}
diff --git a/modules/methyldackel_mbias.nf b/modules/methyldackel_mbias.nf
index 2828b57..e91f314 100644
--- a/modules/methyldackel_mbias.nf
+++ b/modules/methyldackel_mbias.nf
@@ -11,7 +11,7 @@ process methylDackel_mbias {
val(genome_fai)
output:
- path('*.svg'), emit: mbias_output_svg
+ path('*.svg'), optional: true, emit: mbias_output_svg
path('*.tsv'), emit: mbias_output_tsv
tuple val(library), path("${library}.combined_mbias.tsv"), emit: for_agg
tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -n 1 | sed \'s/^samtools //\''), topic: versions
@@ -19,6 +19,7 @@ process methylDackel_mbias {
script:
"""
+ shopt -s nullglob
echo -e "chr\tcontext\tstrand\tRead\tPosition\tnMethylated\tnUnmethylated\tnMethylated(+dups)\tnUnmethylated(+dups)" > ${library}.combined_mbias.tsv
chrs=(`samtools view -H "${md_bam}" | grep @SQ | cut -f 2 | sed 's/SN://'| grep -v _random | grep -v chrUn | sed 's/|/\\|/'`)
diff --git a/modules/picard_metrics.nf b/modules/picard_metrics.nf
index ad64229..da72951 100644
--- a/modules/picard_metrics.nf
+++ b/modules/picard_metrics.nf
@@ -1,5 +1,5 @@
process picard_metrics {
- label 'medium_cpu'
+ label 'single_threaded_qc'
tag { library }
conda "bioconda::picard=3.3.0 bioconda::samtools=1.22"
publishDir "${params.outputDir}/stats/picard_alignment_metrics"
diff --git a/modules/tasmanian.nf b/modules/tasmanian.nf
index 9441c36..09e70cf 100644
--- a/modules/tasmanian.nf
+++ b/modules/tasmanian.nf
@@ -2,11 +2,7 @@ process tasmanian {
label 'medium_cpu'
tag { library }
publishDir "${params.outputDir}/stats/tasmanian"
- conda "bioconda::samtools=1.22 bioconda::tasmanian-mismatch=1.0.9"
-
- errorStrategy { task.attempt <= 1 ? 'retry' : 'terminate' }
- maxRetries 1
- memory { task.attempt > 1 ? '16 GB' : '8 GB' }
+ conda "bioconda::tasmanian-mismatch=2.0.5"
input:
tuple val(library), path(bam), path(bai)
@@ -15,14 +11,11 @@ process tasmanian {
output:
tuple val(library), path("${library}.tasmanian.csv"), emit: for_agg
- tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -n 1 | sed \'s/^samtools //\''), topic: versions
- tuple val("${task.process}"), val('tasmanian'), val('*should be* 1.0.9'), topic: versions
+ tuple val("${task.process}"), val('tasmanian-mismatch'), eval('tasmanian-mismatch --version | cut -f 2 -d " "'), topic: versions
script:
"""
- set +e
- set +o pipefail
- samtools view -q 30 -F 3840 ${bam} | head -n 2000000 | run_tasmanian -r ${genome_fa} > ${library}.tasmanian.csv
+ tasmanian-mismatch --min-base-quality 20 --min-map-quality 30 \\
+ -F 3840 --threads ${task.cpus} -o ${library}.tasmanian.csv ${bam} ${genome_fa}
"""
-
}
diff --git a/modules/trim_and_align.nf b/modules/trim_and_align.nf
new file mode 100644
index 0000000..12fc9cf
--- /dev/null
+++ b/modules/trim_and_align.nf
@@ -0,0 +1,77 @@
+process trimAndAlign {
+ label 'high_cpu'
+ tag { library }
+ conda "conda-forge::python=3.10 bioconda::bwameth=0.2.10 bioconda::mark-nonconverted-reads=1.2 bioconda::samtools=1.22 bioconda::bamslice=0.2.4 bioconda::fgumi=0.7.0"
+ publishDir "${params.outputDir}/bwameth_align", mode: 'symlink'
+
+ input:
+ tuple val(library), path(bam), val(start_offset), val(end_offset)
+ path(adapter_fasta)
+ val(bwa_index)
+ path(genome_fa)
+ path(genome_fai)
+ path(genome_dict)
+
+ output:
+ tuple val(library), path("${chunk}.aln.bam"), emit: bam_files
+ tuple val(library), val(chunk), path("${chunk}.fastp.json"), emit: fastp_json
+ tuple val(library), path("${chunk}.nonconverted_counts.tsv"), emit: nonconverted_counts
+ tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -n 1 | sed \'s/^samtools //\''), topic: versions
+ tuple val("${task.process}"), val('bwameth'), eval("bwameth.py --version | sed 's/^bwa-meth.py //'"), topic: versions
+ tuple val("${task.process}"), val('python'), eval('python --version | sed \'s/^Python //\''), topic: versions
+ tuple val("${task.process}"), val('bamslice'), eval('bamslice --version | cut -f 2 -d " "'), topic: versions
+ tuple val("${task.process}"), val('fgumi'), eval('fgumi --version | cut -f 2 -d " "'), topic: versions
+ tuple val("${task.process}"), val('bamadap'), eval("${params.bamadap_bin} --version | cut -f 2 -d ' '"), topic: versions
+
+ script:
+ chunk = "${library}_${start_offset}_${end_offset}"
+ def trim_cpus = 4
+ def align_cpus = Math.max(1, (task.cpus * 7).intdiv(8))
+ def zip_cpus = 2
+ // Never spills (sort_mem_gb holds the whole chunk), so its real work only starts at
+ // EOF -- after bamadap/bwameth/zipper have already exited and freed their cpus.
+ def sort_cpus = task.cpus
+ def sort_mem_gb = Math.max(1, (task.memory.toGiga() * 5).intdiv(8).intdiv(sort_cpus))
+ def bwameth_pairing = params.single_end ? '' : '-p'
+ def slice_path = "${params.tmp_dir}/${chunk}.slice.bam"
+ """
+ set +o pipefail
+ inst_name=\$(samtools view ${bam} | head -n 1 | cut -d ":" -f 1)
+ rg_line=\$(samtools view -H ${bam} | grep "^@RG" | sed 's/\\t/\\\\t/g' | head -n1)
+ set -o pipefail
+ trim_polyg=\$(echo "\${inst_name}" | awk '{if (\$1~/^A0|^NB|^NS|^VH|^LH/) {print "--trim-poly-g"} else {print ""}}')
+
+ # we write this to a temporary file on local storage so
+ # that both bamadap and fgumi can access it simply
+ bamslice --input ${bam} --start-offset ${start_offset} --end-offset ${end_offset} \\
+ --format bam --output ${slice_path}
+
+ ${params.bamadap_bin} --input ${slice_path} --format fastq --no-mate-suffix \\
+ -l 2 --disable-quality-filtering \\
+ --adapter-fasta ${adapter_fasta} \${trim_polyg} \\
+ --threads ${trim_cpus} --json "${chunk}.fastp.json" \\
+ | bwameth.py -t ${align_cpus} --read-group "\${rg_line}" --reference ${bwa_index} ${bwameth_pairing} - 2> "${library}.log.bwamem" \\
+ | mark-nonconverted-reads.py --reference ${bwa_index} 2> "${chunk}.nonconverted_counts.tsv" \\
+ | fgumi zipper --unmapped ${slice_path} --reference ${genome_fa} \\
+ --exclude-missing-reads true --threads ${zip_cpus} --compression-level 0 \\
+ | samtools sort -T ${params.tmp_dir}/samtools_sort_tmp -@ ${sort_cpus} \\
+ -m ${sort_mem_gb}G -o "${chunk}.aln.bam" /dev/stdin
+
+ rm -f ${slice_path}
+ """
+
+ stub:
+ chunk = "${library}_${start_offset}_${end_offset}"
+ // bamadap/picodup aren't on bioconda yet, so CI can't install real binaries; -stub-run
+ // instead replays real output this exact chunk produced on a genuine (local-machine)
+ // run of the real pipeline against these same fixtures, captured once under
+ // tests/fixtures/stub_outputs/. Regenerate those fixtures if trim_and_align.nf's
+ // logic, its conda pins, or the test fixtures themselves change.
+ def fixture_dir = "${workflow.projectDir}/tests/fixtures/stub_outputs/trim_and_align"
+ """
+ cp ${fixture_dir}/${chunk}.aln.bam .
+ cp ${fixture_dir}/${chunk}.fastp.json .
+ cp ${fixture_dir}/${chunk}.nonconverted_counts.tsv .
+ touch ${library}.log.bwamem
+ """
+}
diff --git a/nextflow.config b/nextflow.config
index 25980c8..1ee0a80 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -6,10 +6,15 @@
----------------------------------------------------------------------------------------
*/
+// Default notification recipient: current OS user with the system's mail domain
+def mailnameFile = new File('/etc/mailname')
+def defaultMailDomain = (mailnameFile.exists() ? mailnameFile.text.trim() : '') ?: java.net.InetAddress.getLocalHost().getCanonicalHostName()
+def defaultEmail = "${System.getProperty('user.name')}@${defaultMailDomain}"
+
// Global default params, used in configs
params {
trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
- email = 'undefined'
+ email = defaultEmail
flowcell = 'undefined'
ubam_dir = './'
workflow = 'EM-seq'
@@ -31,8 +36,20 @@ params {
// null means no cap — per-process defaults in conf/base.config apply.
max_memory = null
+ // Optional cpu cap applied to labeled processes (e.g. --max_cpus 8).
+ // null means no cap — per-process defaults in conf/base.config apply.
+ max_cpus = null
+
+ // Binaries not yet packaged for bioconda; deployed to production via Capistrano
+ // (nebiolabs/bamadap, nebiolabs/picodup). Override with a different absolute path
+ // (e.g. conf/test.config) until bioconda packaging lands.
+ bamadap_bin = '/mnt/bioinfo/prg/bamadap/current/bin/bamadap'
+ picodup_bin = '/mnt/bioinfo/prg/picodup/current/bin/picodup'
+
+ picodup_optical_model = 'ellipse'
+ picodup_optical_distance = null // null => derive from instrument name, as Picard path does
+
// NEB only
- path_to_ngs_agg = null
workflow_name_modifier = null
}
@@ -90,12 +107,6 @@ env {
PYTHONNOUSERSITE = 1
}
-executor {
- name = 'sge'
- queueSize = 10000
- jobName = { "${task.process.tokenize(':')[-1]}" }
-}
-
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
diff --git a/tests/fastq_to_ubam.nf.test.snap b/tests/fastq_to_ubam.nf.test.snap
index f458b9e..545084b 100644
--- a/tests/fastq_to_ubam.nf.test.snap
+++ b/tests/fastq_to_ubam.nf.test.snap
@@ -19,10 +19,10 @@
}
]
],
- "timestamp": "2026-09-09T11:08:21.752408253",
+ "timestamp": "2026-09-07T22:24:27.574255349",
"meta": {
- "nf-test": "0.9.5",
- "nextflow": "24.10.5"
+ "nf-test": "0.9.4",
+ "nextflow": "25.10.4"
}
},
"fastq to uBam workflow - non-standard SRA headers (issue #15)": {
@@ -45,10 +45,10 @@
}
]
],
- "timestamp": "2026-09-09T11:08:29.28099907",
+ "timestamp": "2026-09-07T22:24:36.675298676",
"meta": {
- "nf-test": "0.9.5",
- "nextflow": "24.10.5"
+ "nf-test": "0.9.4",
+ "nextflow": "25.10.4"
}
},
"fastq to uBam workflow - paired-end": {
@@ -71,10 +71,10 @@
}
]
],
- "timestamp": "2026-09-09T11:08:14.201725159",
+ "timestamp": "2026-09-07T22:24:18.57790468",
"meta": {
- "nf-test": "0.9.5",
- "nextflow": "24.10.5"
+ "nf-test": "0.9.4",
+ "nextflow": "25.10.4"
}
}
}
\ No newline at end of file
diff --git a/tests/fixtures/reference_files/reference.dict b/tests/fixtures/reference_files/reference.dict
new file mode 100644
index 0000000..918b1b0
--- /dev/null
+++ b/tests/fixtures/reference_files/reference.dict
@@ -0,0 +1,2 @@
+@HD VN:1.0 SO:unsorted
+@SQ SN:chr1 LN:284940 M5:e2d98a7cc072e12f74f7ef08529c1cba UR:file:///appdev/langhorst/src/EM-seq/tests/fixtures/reference_files/reference.fa
diff --git a/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.ds.1.markdups_log b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.ds.1.markdups_log
new file mode 100644
index 0000000..10ff3b3
--- /dev/null
+++ b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.ds.1.markdups_log
@@ -0,0 +1,10 @@
+## htsjdk.samtools.metrics.StringHeader
+# /appdev/langhorst/src/picodup/target-el8/release/picodup --input /dev/stdin --output emseq-test1.ds.1.md.bam --metrics emseq-test1.ds.1.markdups_log --threads 14 --optical-model ellipse --optical-distance 2500 --tagging-policy All
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Mon Sep 07 22:25:49 EDT 2026
+
+## METRICS CLASS picard.sam.DuplicationMetrics
+LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
+emseq-test1.ds.1 745 0 18 0 14 0 0 0.018792
+
+
diff --git a/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.ds.1.md.bai b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.ds.1.md.bai
new file mode 100644
index 0000000..68ffd4f
Binary files /dev/null and b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.ds.1.md.bai differ
diff --git a/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.ds.1.md.bam b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.ds.1.md.bam
new file mode 100644
index 0000000..b528f79
Binary files /dev/null and b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.ds.1.md.bam differ
diff --git a/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.markdups_log b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.markdups_log
new file mode 100644
index 0000000..507e936
--- /dev/null
+++ b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.markdups_log
@@ -0,0 +1,13 @@
+## htsjdk.samtools.metrics.StringHeader
+# /appdev/langhorst/src/picodup/target-el8/release/picodup --input /dev/stdin --output emseq-test1.md.bam --metrics emseq-test1.markdups_log --threads 14 --optical-model ellipse --optical-distance 100 --tagging-policy All
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Mon Sep 07 22:25:29 EDT 2026
+
+## METRICS CLASS picard.sam.DuplicationMetrics
+LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
+Oct25_PV_10ngR3_F6 264 635 1 264 24 0 0 0.015645
+
+## HISTOGRAM java.lang.Double
+BIN CoverageMult all_sets optical_sets non_optical_sets
+1.0 0.000000 623 0 623
+
diff --git a/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.md.bai b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.md.bai
new file mode 100644
index 0000000..cc29ca9
Binary files /dev/null and b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.md.bai differ
diff --git a/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.md.bam b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.md.bam
new file mode 100644
index 0000000..de14fcb
Binary files /dev/null and b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test1.md.bam differ
diff --git a/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.ds.1.markdups_log b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.ds.1.markdups_log
new file mode 100644
index 0000000..8b1b551
--- /dev/null
+++ b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.ds.1.markdups_log
@@ -0,0 +1,10 @@
+## htsjdk.samtools.metrics.StringHeader
+# /appdev/langhorst/src/picodup/target-el8/release/picodup --input /dev/stdin --output emseq-test2.ds.1.md.bam --metrics emseq-test2.ds.1.markdups_log --threads 14 --optical-model ellipse --optical-distance 2500 --tagging-policy All
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Mon Sep 07 22:25:49 EDT 2026
+
+## METRICS CLASS picard.sam.DuplicationMetrics
+LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
+emseq-test2.ds.1 48 0 0 0 0 0 0 0.000000
+
+
diff --git a/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.ds.1.md.bai b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.ds.1.md.bai
new file mode 100644
index 0000000..f094e5f
Binary files /dev/null and b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.ds.1.md.bai differ
diff --git a/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.ds.1.md.bam b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.ds.1.md.bam
new file mode 100644
index 0000000..70de194
Binary files /dev/null and b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.ds.1.md.bam differ
diff --git a/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.markdups_log b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.markdups_log
new file mode 100644
index 0000000..e6b775e
--- /dev/null
+++ b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.markdups_log
@@ -0,0 +1,13 @@
+## htsjdk.samtools.metrics.StringHeader
+# /appdev/langhorst/src/picodup/target-el8/release/picodup --input /dev/stdin --output emseq-test2.md.bam --metrics emseq-test2.markdups_log --threads 14 --optical-model ellipse --optical-distance 100 --tagging-policy All
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Mon Sep 07 22:25:29 EDT 2026
+
+## METRICS CLASS picard.sam.DuplicationMetrics
+LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
+Oct25_PV_10ngR3_F6 264 635 1 264 23 0 0 0.014993
+
+## HISTOGRAM java.lang.Double
+BIN CoverageMult all_sets optical_sets non_optical_sets
+1.0 0.000000 624 0 624
+
diff --git a/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.md.bai b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.md.bai
new file mode 100644
index 0000000..0fb78c3
Binary files /dev/null and b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.md.bai differ
diff --git a/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.md.bam b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.md.bam
new file mode 100644
index 0000000..a5dc419
Binary files /dev/null and b/tests/fixtures/stub_outputs/merge_and_picodup/emseq-test2.md.bam differ
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test1.ds.1_0_257200.aln.bam b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1.ds.1_0_257200.aln.bam
new file mode 100644
index 0000000..f84c365
Binary files /dev/null and b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1.ds.1_0_257200.aln.bam differ
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test1.ds.1_0_257200.fastp.json b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1.ds.1_0_257200.fastp.json
new file mode 100644
index 0000000..397f181
--- /dev/null
+++ b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1.ds.1_0_257200.fastp.json
@@ -0,0 +1,5510 @@
+{
+ "summary": {
+ "bamadap_version": "0.1.0",
+ "fastp_version": "0.1.0",
+ "sequencing": "single end (150 cycles)",
+ "before_filtering": {
+ "total_reads": 2500,
+ "total_bases": 375000,
+ "q20_bases": 368284,
+ "q30_bases": 356222,
+ "q20_rate": 0.9820906666666667,
+ "q30_rate": 0.9499253333333333,
+ "read1_mean_length": 150,
+ "gc_content": 0.21490933333333334
+ },
+ "after_filtering": {
+ "total_reads": 2500,
+ "total_bases": 371387,
+ "q20_bases": 364731,
+ "q30_bases": 352753,
+ "q20_rate": 0.9820779941139566,
+ "q30_rate": 0.9498259228244392,
+ "read1_mean_length": 148,
+ "gc_content": 0.21198103326179968
+ }
+ },
+ "filtering_result": {
+ "passed_filter_reads": 2500,
+ "low_quality_reads": 0,
+ "too_many_N_reads": 0,
+ "adapter_dimer_reads": 0,
+ "too_short_reads": 0,
+ "too_long_reads": 0,
+ "low_complexity_reads": 0
+ },
+ "duplication": {
+ "rate": 0.0
+ },
+ "adapter_cutting": {
+ "adapter_trimmed_reads": 156,
+ "adapter_trimmed_bases": 3613,
+ "read1_adapter_sequence": "AGATCGGAAGAGC",
+ "read2_adapter_sequence": "AGATCGGAAGAGC",
+ "read1_adapter_counts": {
+ "AGATC": 6,
+ "AGATCG": 7,
+ "AGATCGG": 6,
+ "AGATCGGA": 4,
+ "AGATCGGAA": 6,
+ "AGATCGGAAG": 7,
+ "AGATCGGAAGA": 7,
+ "AGATCGGAAGAG": 7,
+ "AGATCGGAAGAGC": 6,
+ "AGATCGGAAGAGCA": 6,
+ "AGATCGGAAGAGCAC": 2,
+ "AGATCGGAAGAGCACA": 5,
+ "AGATCGGAAGAGCACAC": 6,
+ "AGATCGGAAGAGCACACG": 3,
+ "AGATCGGAAGAGCACACGT": 2,
+ "AGATCGGAAGAGCACACGTC": 2,
+ "AGATCGGAAGAGCACACGTCT": 4,
+ "AGATCGGAAGAGCACACGTCTG": 4,
+ "AGATCGGAAGAGCACACGTCTGA": 2,
+ "AGATCGGAAGAGCACACGTCTGAAC": 3,
+ "AGATCGGAAGAGCACACGTCTGAACT": 4,
+ "AGATCGGAAGAGCACACGTCTGAACTC": 3,
+ "AGATCGGAAGAGCACACGTCTGAACTCC": 6,
+ "AGATCGGAAGAGCACACGTCTGAACTCCA": 3,
+ "AGATCGGAAGAGCACACGTCTGAACTCCAG": 2,
+ "AGATCGGAAGAGCACACGTCTGAACTCCAGTC": 3,
+ "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC": 2,
+ "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACG": 3,
+ "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCTTC": 2,
+ "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCTTCACA": 2,
+ "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCTTCACAA": 2,
+ "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCTTCACAATCTCGTAT": 3,
+ "others": 26
+ },
+ "read2_adapter_counts": {
+ "others": 0
+ },
+ "extra_adapter_sequences": [
+ "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
+ "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"
+ ]
+ },
+ "read1_before_filtering": {
+ "total_reads": 2500,
+ "total_bases": 375000,
+ "q20_bases": 368284,
+ "q30_bases": 356222,
+ "q40_bases": 321227,
+ "total_cycles": 150,
+ "quality_curves": {
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+ "command": "/appdev/langhorst/src/bamadap/target-el8/release/bamadap --input /tmp/emseq-test1.ds.1_0_257200.slice.bam --format fastq --no-mate-suffix -l 2 --disable-quality-filtering --adapter-fasta illumina_adapters.fa --threads 4 --json emseq-test1.ds.1_0_257200.fastp.json"
+}
\ No newline at end of file
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test1.ds.1_0_257200.nonconverted_counts.tsv b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1.ds.1_0_257200.nonconverted_counts.tsv
new file mode 100644
index 0000000..4b1db9b
--- /dev/null
+++ b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1.ds.1_0_257200.nonconverted_counts.tsv
@@ -0,0 +1 @@
+chr1 0
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_0_250000.aln.bam b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_0_250000.aln.bam
new file mode 100644
index 0000000..0f4388e
Binary files /dev/null and b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_0_250000.aln.bam differ
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_0_250000.fastp.json b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_0_250000.fastp.json
new file mode 100644
index 0000000..0c4f080
--- /dev/null
+++ b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_0_250000.fastp.json
@@ -0,0 +1,8219 @@
+{
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+ },
+ "overrepresented_sequences": {}
+ },
+ "command": "/appdev/langhorst/src/bamadap/target-el8/release/bamadap --input /tmp/emseq-test1_0_250000.slice.bam --format fastq --no-mate-suffix -l 2 --disable-quality-filtering --adapter-fasta illumina_adapters.fa --trim-poly-g --threads 4 --json emseq-test1_0_250000.fastp.json"
+}
\ No newline at end of file
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_0_250000.nonconverted_counts.tsv b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_0_250000.nonconverted_counts.tsv
new file mode 100644
index 0000000..4b1db9b
--- /dev/null
+++ b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_0_250000.nonconverted_counts.tsv
@@ -0,0 +1 @@
+chr1 0
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_250000_421605.aln.bam b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_250000_421605.aln.bam
new file mode 100644
index 0000000..734fe90
Binary files /dev/null and b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_250000_421605.aln.bam differ
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_250000_421605.fastp.json b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_250000_421605.fastp.json
new file mode 100644
index 0000000..4fcaf3b
--- /dev/null
+++ b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_250000_421605.fastp.json
@@ -0,0 +1,8205 @@
+{
+ "summary": {
+ "bamadap_version": "0.1.0",
+ "fastp_version": "0.1.0",
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+ "q20_bases": 275601,
+ "q30_bases": 268156,
+ "q20_rate": 0.9409260371999016,
+ "q30_rate": 0.9155081528418868,
+ "read1_mean_length": 76,
+ "read2_mean_length": 76,
+ "gc_content": 0.21639513287630077
+ },
+ "after_filtering": {
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+ "q20_bases": 273935,
+ "q30_bases": 266561,
+ "q20_rate": 0.941897927676708,
+ "q30_rate": 0.9165431708231184,
+ "read1_mean_length": 75,
+ "read2_mean_length": 75,
+ "gc_content": 0.21431543188015115
+ }
+ },
+ "filtering_result": {
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+ "low_complexity_reads": 0
+ },
+ "duplication": {
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+ "GGTAA": 0,
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+ "GGTAC": 0,
+ "GGTAG": 0,
+ "GGTTA": 0,
+ "GGTTT": 0,
+ "GGTTC": 0,
+ "GGTTG": 0,
+ "GGTCA": 0,
+ "GGTCT": 0,
+ "GGTCC": 0,
+ "GGTCG": 0,
+ "GGTGA": 0,
+ "GGTGT": 0,
+ "GGTGC": 0,
+ "GGTGG": 0,
+ "GGCAA": 0,
+ "GGCAT": 0,
+ "GGCAC": 0,
+ "GGCAG": 0,
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+ "GGCTT": 0,
+ "GGCTC": 0,
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+ "GGCGT": 0,
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+ "GGGCT": 0,
+ "GGGCC": 0,
+ "GGGCG": 0,
+ "GGGGA": 0,
+ "GGGGT": 0,
+ "GGGGC": 0,
+ "GGGGG": 0
+ },
+ "overrepresented_sequences": {}
+ },
+ "command": "/appdev/langhorst/src/bamadap/target-el8/release/bamadap --input /tmp/emseq-test1_250000_421605.slice.bam --format fastq --no-mate-suffix -l 2 --disable-quality-filtering --adapter-fasta illumina_adapters.fa --trim-poly-g --threads 4 --json emseq-test1_250000_421605.fastp.json"
+}
\ No newline at end of file
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_250000_421605.nonconverted_counts.tsv b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_250000_421605.nonconverted_counts.tsv
new file mode 100644
index 0000000..4b1db9b
--- /dev/null
+++ b/tests/fixtures/stub_outputs/trim_and_align/emseq-test1_250000_421605.nonconverted_counts.tsv
@@ -0,0 +1 @@
+chr1 0
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test2.ds.1_0_16821.aln.bam b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2.ds.1_0_16821.aln.bam
new file mode 100644
index 0000000..ac12614
Binary files /dev/null and b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2.ds.1_0_16821.aln.bam differ
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test2.ds.1_0_16821.fastp.json b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2.ds.1_0_16821.fastp.json
new file mode 100644
index 0000000..9719ab6
--- /dev/null
+++ b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2.ds.1_0_16821.fastp.json
@@ -0,0 +1,4387 @@
+{
+ "summary": {
+ "bamadap_version": "0.1.0",
+ "fastp_version": "0.1.0",
+ "sequencing": "single end (99 cycles)",
+ "before_filtering": {
+ "total_reads": 369,
+ "total_bases": 36531,
+ "q20_bases": 36142,
+ "q30_bases": 35164,
+ "q20_rate": 0.9893515096767129,
+ "q30_rate": 0.962579726807369,
+ "read1_mean_length": 99,
+ "gc_content": 0.2288741069228874
+ },
+ "after_filtering": {
+ "total_reads": 369,
+ "total_bases": 35186,
+ "q20_bases": 34807,
+ "q30_bases": 33870,
+ "q20_rate": 0.9892286704939465,
+ "q30_rate": 0.9625987608708009,
+ "read1_mean_length": 95,
+ "gc_content": 0.21767180128460184
+ }
+ },
+ "filtering_result": {
+ "passed_filter_reads": 369,
+ "low_quality_reads": 0,
+ "too_many_N_reads": 0,
+ "adapter_dimer_reads": 0,
+ "too_short_reads": 0,
+ "too_long_reads": 0,
+ "low_complexity_reads": 0
+ },
+ "duplication": {
+ "rate": 0.0
+ },
+ "adapter_cutting": {
+ "adapter_trimmed_reads": 60,
+ "adapter_trimmed_bases": 1345,
+ "read1_adapter_sequence": "AGATCGGAAGAGC",
+ "read2_adapter_sequence": "AGATCGGAAGAGC",
+ "read1_adapter_counts": {
+ "AGATCG": 4,
+ "AGATCGG": 3,
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+ },
+ "overrepresented_sequences": {}
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+ "command": "/appdev/langhorst/src/bamadap/target-el8/release/bamadap --input /tmp/emseq-test2.ds.1_0_16821.slice.bam --format fastq --no-mate-suffix -l 2 --disable-quality-filtering --adapter-fasta illumina_adapters.fa --trim-poly-g --threads 4 --json emseq-test2.ds.1_0_16821.fastp.json"
+}
\ No newline at end of file
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test2.ds.1_0_16821.nonconverted_counts.tsv b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2.ds.1_0_16821.nonconverted_counts.tsv
new file mode 100644
index 0000000..4b1db9b
--- /dev/null
+++ b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2.ds.1_0_16821.nonconverted_counts.tsv
@@ -0,0 +1 @@
+chr1 0
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_0_250000.aln.bam b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_0_250000.aln.bam
new file mode 100644
index 0000000..7d2de7a
Binary files /dev/null and b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_0_250000.aln.bam differ
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_0_250000.fastp.json b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_0_250000.fastp.json
new file mode 100644
index 0000000..27b66cf
--- /dev/null
+++ b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_0_250000.fastp.json
@@ -0,0 +1,8219 @@
+{
+ "summary": {
+ "bamadap_version": "0.1.0",
+ "fastp_version": "0.1.0",
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+ "q20_rate": 0.9390891401037805,
+ "q30_rate": 0.9126389918458118,
+ "read1_mean_length": 76,
+ "read2_mean_length": 76,
+ "gc_content": 0.22025574499629355
+ },
+ "after_filtering": {
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+ "q20_bases": 402675,
+ "q30_bases": 391415,
+ "q20_rate": 0.9397667124093315,
+ "q30_rate": 0.913488018222384,
+ "read1_mean_length": 75,
+ "read2_mean_length": 75,
+ "gc_content": 0.21852391221142448
+ }
+ },
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+ "low_complexity_reads": 0
+ },
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+ "GGTAC": 0,
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+ "GGTTA": 0,
+ "GGTTT": 0,
+ "GGTTC": 0,
+ "GGTTG": 0,
+ "GGTCA": 0,
+ "GGTCT": 0,
+ "GGTCC": 0,
+ "GGTCG": 0,
+ "GGTGA": 0,
+ "GGTGT": 0,
+ "GGTGC": 0,
+ "GGTGG": 0,
+ "GGCAA": 0,
+ "GGCAT": 0,
+ "GGCAC": 0,
+ "GGCAG": 0,
+ "GGCTA": 0,
+ "GGCTT": 0,
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+ "GGCGA": 0,
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+ "GGGCT": 0,
+ "GGGCC": 0,
+ "GGGCG": 0,
+ "GGGGA": 0,
+ "GGGGT": 0,
+ "GGGGC": 0,
+ "GGGGG": 0
+ },
+ "overrepresented_sequences": {}
+ },
+ "command": "/appdev/langhorst/src/bamadap/target-el8/release/bamadap --input /tmp/emseq-test2_0_250000.slice.bam --format fastq --no-mate-suffix -l 2 --disable-quality-filtering --adapter-fasta illumina_adapters.fa --trim-poly-g --threads 4 --json emseq-test2_0_250000.fastp.json"
+}
\ No newline at end of file
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_0_250000.nonconverted_counts.tsv b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_0_250000.nonconverted_counts.tsv
new file mode 100644
index 0000000..4b1db9b
--- /dev/null
+++ b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_0_250000.nonconverted_counts.tsv
@@ -0,0 +1 @@
+chr1 0
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_250000_426231.aln.bam b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_250000_426231.aln.bam
new file mode 100644
index 0000000..7d73370
Binary files /dev/null and b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_250000_426231.aln.bam differ
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_250000_426231.fastp.json b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_250000_426231.fastp.json
new file mode 100644
index 0000000..a0fe1cd
--- /dev/null
+++ b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_250000_426231.fastp.json
@@ -0,0 +1,8205 @@
+{
+ "summary": {
+ "bamadap_version": "0.1.0",
+ "fastp_version": "0.1.0",
+ "sequencing": "paired end (76 cycles + 76 cycles)",
+ "before_filtering": {
+ "total_reads": 3852,
+ "total_bases": 292752,
+ "q20_bases": 275514,
+ "q30_bases": 268079,
+ "q20_rate": 0.9411173962944746,
+ "q30_rate": 0.9157204733016342,
+ "read1_mean_length": 76,
+ "read2_mean_length": 76,
+ "gc_content": 0.21632986281904137
+ },
+ "after_filtering": {
+ "total_reads": 3846,
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+ "GTACC": 0,
+ "GTACG": 0,
+ "GTAGA": 0,
+ "GTAGT": 0,
+ "GTAGC": 0,
+ "GTAGG": 0,
+ "GTTAA": 0,
+ "GTTAT": 0,
+ "GTTAC": 0,
+ "GTTAG": 0,
+ "GTTTA": 0,
+ "GTTTT": 0,
+ "GTTTC": 0,
+ "GTTTG": 0,
+ "GTTCA": 0,
+ "GTTCT": 0,
+ "GTTCC": 0,
+ "GTTCG": 0,
+ "GTTGA": 0,
+ "GTTGT": 0,
+ "GTTGC": 0,
+ "GTTGG": 0,
+ "GTCAA": 0,
+ "GTCAT": 0,
+ "GTCAC": 0,
+ "GTCAG": 0,
+ "GTCTA": 0,
+ "GTCTT": 0,
+ "GTCTC": 0,
+ "GTCTG": 0,
+ "GTCCA": 0,
+ "GTCCT": 0,
+ "GTCCC": 0,
+ "GTCCG": 0,
+ "GTCGA": 0,
+ "GTCGT": 0,
+ "GTCGC": 0,
+ "GTCGG": 0,
+ "GTGAA": 0,
+ "GTGAT": 0,
+ "GTGAC": 0,
+ "GTGAG": 0,
+ "GTGTA": 0,
+ "GTGTT": 0,
+ "GTGTC": 0,
+ "GTGTG": 0,
+ "GTGCA": 0,
+ "GTGCT": 0,
+ "GTGCC": 0,
+ "GTGCG": 0,
+ "GTGGA": 0,
+ "GTGGT": 0,
+ "GTGGC": 0,
+ "GTGGG": 0,
+ "GCAAA": 0,
+ "GCAAT": 0,
+ "GCAAC": 0,
+ "GCAAG": 0,
+ "GCATA": 0,
+ "GCATT": 0,
+ "GCATC": 0,
+ "GCATG": 0,
+ "GCACA": 0,
+ "GCACT": 0,
+ "GCACC": 0,
+ "GCACG": 0,
+ "GCAGA": 0,
+ "GCAGT": 0,
+ "GCAGC": 0,
+ "GCAGG": 0,
+ "GCTAA": 0,
+ "GCTAT": 0,
+ "GCTAC": 0,
+ "GCTAG": 0,
+ "GCTTA": 0,
+ "GCTTT": 0,
+ "GCTTC": 0,
+ "GCTTG": 0,
+ "GCTCA": 0,
+ "GCTCT": 0,
+ "GCTCC": 0,
+ "GCTCG": 0,
+ "GCTGA": 0,
+ "GCTGT": 0,
+ "GCTGC": 0,
+ "GCTGG": 0,
+ "GCCAA": 0,
+ "GCCAT": 0,
+ "GCCAC": 0,
+ "GCCAG": 0,
+ "GCCTA": 0,
+ "GCCTT": 0,
+ "GCCTC": 0,
+ "GCCTG": 0,
+ "GCCCA": 0,
+ "GCCCT": 0,
+ "GCCCC": 0,
+ "GCCCG": 0,
+ "GCCGA": 0,
+ "GCCGT": 0,
+ "GCCGC": 0,
+ "GCCGG": 0,
+ "GCGAA": 0,
+ "GCGAT": 0,
+ "GCGAC": 0,
+ "GCGAG": 0,
+ "GCGTA": 0,
+ "GCGTT": 0,
+ "GCGTC": 0,
+ "GCGTG": 0,
+ "GCGCA": 0,
+ "GCGCT": 0,
+ "GCGCC": 0,
+ "GCGCG": 0,
+ "GCGGA": 0,
+ "GCGGT": 0,
+ "GCGGC": 0,
+ "GCGGG": 0,
+ "GGAAA": 0,
+ "GGAAT": 0,
+ "GGAAC": 0,
+ "GGAAG": 0,
+ "GGATA": 0,
+ "GGATT": 0,
+ "GGATC": 0,
+ "GGATG": 0,
+ "GGACA": 0,
+ "GGACT": 0,
+ "GGACC": 0,
+ "GGACG": 0,
+ "GGAGA": 0,
+ "GGAGT": 0,
+ "GGAGC": 0,
+ "GGAGG": 0,
+ "GGTAA": 0,
+ "GGTAT": 0,
+ "GGTAC": 0,
+ "GGTAG": 0,
+ "GGTTA": 0,
+ "GGTTT": 0,
+ "GGTTC": 0,
+ "GGTTG": 0,
+ "GGTCA": 0,
+ "GGTCT": 0,
+ "GGTCC": 0,
+ "GGTCG": 0,
+ "GGTGA": 0,
+ "GGTGT": 0,
+ "GGTGC": 0,
+ "GGTGG": 0,
+ "GGCAA": 0,
+ "GGCAT": 0,
+ "GGCAC": 0,
+ "GGCAG": 0,
+ "GGCTA": 0,
+ "GGCTT": 0,
+ "GGCTC": 0,
+ "GGCTG": 0,
+ "GGCCA": 0,
+ "GGCCT": 0,
+ "GGCCC": 0,
+ "GGCCG": 0,
+ "GGCGA": 0,
+ "GGCGT": 0,
+ "GGCGC": 0,
+ "GGCGG": 0,
+ "GGGAA": 0,
+ "GGGAT": 0,
+ "GGGAC": 0,
+ "GGGAG": 0,
+ "GGGTA": 0,
+ "GGGTT": 0,
+ "GGGTC": 0,
+ "GGGTG": 0,
+ "GGGCA": 0,
+ "GGGCT": 0,
+ "GGGCC": 0,
+ "GGGCG": 0,
+ "GGGGA": 0,
+ "GGGGT": 0,
+ "GGGGC": 0,
+ "GGGGG": 0
+ },
+ "overrepresented_sequences": {}
+ },
+ "command": "/appdev/langhorst/src/bamadap/target-el8/release/bamadap --input /tmp/emseq-test2_250000_426231.slice.bam --format fastq --no-mate-suffix -l 2 --disable-quality-filtering --adapter-fasta illumina_adapters.fa --trim-poly-g --threads 4 --json emseq-test2_250000_426231.fastp.json"
+}
\ No newline at end of file
diff --git a/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_250000_426231.nonconverted_counts.tsv b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_250000_426231.nonconverted_counts.tsv
new file mode 100644
index 0000000..4b1db9b
--- /dev/null
+++ b/tests/fixtures/stub_outputs/trim_and_align/emseq-test2_250000_426231.nonconverted_counts.tsv
@@ -0,0 +1 @@
+chr1 0
diff --git a/tests/main.nf.test b/tests/main.nf.test
index 2a63a78..d9f48e6 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -76,11 +76,11 @@ nextflow_pipeline {
test("EM-seq workflow uBam - single-end") {
when {
- params.ubam_dir = "$projectDir/tests/fixtures/ubam/"
+ params.ubam_dir = "$projectDir/tests/fixtures/ubam_single_end/"
params.genome = 'test'
params.email = 'foo@example.com'
params.flowcell = "test_pipeline"
- params.bamslice_chunk_size = 250000
+ params.bamslice_chunk_size = 300000
params.enable_neb_agg = true
params.single_end = true
params.adapter_set = "test"
@@ -88,34 +88,32 @@ nextflow_pipeline {
}
then {
- def bwameth_file_1 = bam("${launchDir}/test_output/bwameth_align/emseq-test1_0_250000.aln.bam").getStatistics()
- def bwameth_file_2 = bam("${launchDir}/test_output/bwameth_align/emseq-test1_250000_421605.aln.bam").getStatistics()
- def fastqc = path("${launchDir}/test_output/stats/fastqc/emseq-test1.md_fastqc.html").exists()
- def fastp = path("${launchDir}/test_output/fastp/emseq-test1.fastp.json").text.tokenize('\n')[1..33]
- def markdup = bam("${launchDir}/test_output/markduped_bams/emseq-test1.md.bam").getStatistics()
- def markdup_log = path("${launchDir}/test_output/stats/markdups/emseq-test1.markdups_log").text.tokenize('\n')[5..6]
- def idxstats = path("${launchDir}/test_output/stats/idxstats/emseq-test1.idxstat").text.tokenize('\n')
- def flagstats = path("${launchDir}/test_output/stats/flagstats/emseq-test1.flagstat").text.tokenize('\n')
- def gc_bias = path("${launchDir}/test_output/stats/gc_bias/emseq-test1.gc_metrics").text.tokenize('\n')[5..-1]
- def gc_bias_groups = path("${launchDir}/test_output/stats/gc_bias/emseq-test1.gc_metrics.combined.tsv").text.tokenize('\n').findAll { !it.startsWith('#') && it.trim() }
- def alignment_metrics = path("${launchDir}/test_output/stats/picard_alignment_metrics/emseq-test1.alignment_summary_metrics.txt").text.tokenize('\n')[5..8]
- def methyldackel_extract = path("${launchDir}/test_output/methylDackelExtracts/emseq-test1_CpG.methylKit.gz").md5
- def mbias = path("${launchDir}/test_output/methylDackelExtracts/mbias/emseq-test1.combined_mbias.tsv").md5
- def nonconverted = path("${launchDir}/test_output/bwameth_align/emseq-test1_0_250000.nonconverted_counts.tsv").text.tokenize('\n')
- def nonconverted_combined = path("${launchDir}/test_output/stats/nonconverted_counts/emseq-test1.nonconverted_counts.for_agg.tsv").text.tokenize('\n')
+ def bwameth_file_1 = bam("${launchDir}/test_output/bwameth_align/emseq-test1.ds.1_0_257200.aln.bam").getStatistics()
+ def fastqc = path("${launchDir}/test_output/stats/fastqc/emseq-test1.ds.1.md_fastqc.html").exists()
+ def fastp = path("${launchDir}/test_output/fastp/emseq-test1.ds.1.fastp.json").text.tokenize('\n')[1..33]
+ def markdup = bam("${launchDir}/test_output/markduped_bams/emseq-test1.ds.1.md.bam").getStatistics()
+ def markdup_log = path("${launchDir}/test_output/stats/markdups/emseq-test1.ds.1.markdups_log").text.tokenize('\n')[5..6]
+ def idxstats = path("${launchDir}/test_output/stats/idxstats/emseq-test1.ds.1.idxstat").text.tokenize('\n')
+ def flagstats = path("${launchDir}/test_output/stats/flagstats/emseq-test1.ds.1.flagstat").text.tokenize('\n')
+ def gc_bias = path("${launchDir}/test_output/stats/gc_bias/emseq-test1.ds.1.gc_metrics").text.tokenize('\n')[5..-1]
+ def gc_bias_groups = path("${launchDir}/test_output/stats/gc_bias/emseq-test1.ds.1.gc_metrics.combined.tsv").text.tokenize('\n').findAll { !it.startsWith('#') && it.trim() }
+ def alignment_metrics = path("${launchDir}/test_output/stats/picard_alignment_metrics/emseq-test1.ds.1.alignment_summary_metrics.txt").text.tokenize('\n')[5..8]
+ def methyldackel_extract = path("${launchDir}/test_output/methylDackelExtracts/emseq-test1.ds.1_CpG.methylKit.gz").md5
+ def mbias = path("${launchDir}/test_output/methylDackelExtracts/mbias/emseq-test1.ds.1.combined_mbias.tsv").md5
+ def nonconverted = path("${launchDir}/test_output/bwameth_align/emseq-test1.ds.1_0_257200.nonconverted_counts.tsv").text.tokenize('\n')
+ def nonconverted_combined = path("${launchDir}/test_output/stats/nonconverted_counts/emseq-test1.ds.1.nonconverted_counts.for_agg.tsv").text.tokenize('\n')
def combined_summaries = path("${launchDir}/test_output/methylKit_intersections/positional_summaries_combined.tsv").exists()
- def positional_summary = path("${launchDir}/test_output/methylKit_intersections/emseq-test1_vs_emseq_test_regions_positional_summary.tsv").text.tokenize('\n')
- def methylkit_intersections = path("${launchDir}/test_output/methylKit_intersections/emseq-test2_vs_emseq_test_regions_intersections.tsv").text.tokenize('\n')
- def region_summary = path("${launchDir}/test_output/methylKit_intersections/emseq-test2_vs_emseq_test_regions_region_summary.tsv").text.tokenize('\n')
- def tasmanian = path("${launchDir}/test_output/stats/tasmanian/emseq-test1.tasmanian.csv").exists()
+ def positional_summary = path("${launchDir}/test_output/methylKit_intersections/emseq-test1.ds.1_vs_emseq_test_regions_positional_summary.tsv").text.tokenize('\n')
+ def methylkit_intersections = path("${launchDir}/test_output/methylKit_intersections/emseq-test2.ds.1_vs_emseq_test_regions_intersections.tsv").text.tokenize('\n')
+ def region_summary = path("${launchDir}/test_output/methylKit_intersections/emseq-test2.ds.1_vs_emseq_test_regions_region_summary.tsv").text.tokenize('\n')
+ def tasmanian = path("${launchDir}/test_output/stats/tasmanian/emseq-test1.ds.1.tasmanian.csv").exists()
def multiqc = path("${launchDir}/test_output/EM-seq-Alignment-Summary-test_pipeline_multiqc_report.html").exists()
- def ngs_agg = path("${launchDir}/test_output/aggregate_results/emseq-test1.arguments.txt").text.tokenize('\n')
+ def ngs_agg = path("${launchDir}/test_output/aggregate_results/emseq-test1.ds.1.arguments.txt").text.tokenize('\n')
assertAll(
{ assert workflow.success },
{ assert snapshot(workflow.trace,
["bwameth_file_1", bwameth_file_1],
- ["bwameth_file_2", bwameth_file_2],
["fastqc", fastqc],
["fastp", fastp],
["markdup", markdup],
diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
index 8075cfa..e2e92d8 100644
--- a/tests/main.nf.test.snap
+++ b/tests/main.nf.test.snap
@@ -2,32 +2,20 @@
"EM-seq workflow uBam - single-end": {
"content": [
{
- "tasksCount": 51,
+ "tasksCount": 45,
"tasksFailed": 0,
- "tasksSucceeded": 51
+ "tasksSucceeded": 45
},
[
"bwameth_file_1",
{
- "maxReadLength": 76,
- "minReadLength": 44,
- "meanReadLength": 75,
- "maxQuality": 60,
- "minQuality": 0,
- "meanQuality": 10,
- "readCount": 702
- }
- ],
- [
- "bwameth_file_2",
- {
- "maxReadLength": 76,
- "minReadLength": 52,
- "meanReadLength": 75,
+ "maxReadLength": 150,
+ "minReadLength": 53,
+ "meanReadLength": 146,
"maxQuality": 60,
"minQuality": 0,
- "meanQuality": 8,
- "readCount": 399
+ "meanQuality": 41,
+ "readCount": 763
}
],
[
@@ -38,35 +26,35 @@
"fastp",
[
"\t\"summary\": {",
- "\t\t\"fastp_version\": \"1.3.6\",",
- "\t\t\"sequencing\": \"single end (76 cycles)\",",
+ "\t\t\"fastp_version\": \"0.1.0\",",
+ "\t\t\"sequencing\": \"single end (150 cycles)\",",
"\t\t\"before_filtering\": {",
- "\t\t\t\"total_reads\": 9534,",
- "\t\t\t\"total_bases\": 724584,",
- "\t\t\t\"q20_bases\": 681052,",
- "\t\t\t\"q30_bases\": 662196,",
- "\t\t\t\"q20_rate\": 0.939921,",
- "\t\t\t\"q30_rate\": 0.913898,",
- "\t\t\t\"read1_mean_length\": 76,",
- "\t\t\t\"gc_content\": 0.218667",
+ "\t\t\t\"total_reads\": 2500,",
+ "\t\t\t\"total_bases\": 375000,",
+ "\t\t\t\"q20_bases\": 368284,",
+ "\t\t\t\"q30_bases\": 356222,",
+ "\t\t\t\"q20_rate\": 0.982091,",
+ "\t\t\t\"q30_rate\": 0.949925,",
+ "\t\t\t\"read1_mean_length\": 150,",
+ "\t\t\t\"gc_content\": 0.214909",
"\t\t},",
"\t\t\"after_filtering\": {",
- "\t\t\t\"total_reads\": 9530,",
- "\t\t\t\"total_bases\": 721079,",
- "\t\t\t\"q20_bases\": 678095,",
- "\t\t\t\"q30_bases\": 659406,",
- "\t\t\t\"q20_rate\": 0.940389,",
- "\t\t\t\"q30_rate\": 0.914471,",
- "\t\t\t\"read1_mean_length\": 75,",
- "\t\t\t\"gc_content\": 0.216831",
+ "\t\t\t\"total_reads\": 2500,",
+ "\t\t\t\"total_bases\": 371387,",
+ "\t\t\t\"q20_bases\": 364731,",
+ "\t\t\t\"q30_bases\": 352753,",
+ "\t\t\t\"q20_rate\": 0.982078,",
+ "\t\t\t\"q30_rate\": 0.949826,",
+ "\t\t\t\"read1_mean_length\": 148,",
+ "\t\t\t\"gc_content\": 0.211981",
"\t\t}",
"\t},",
"\t\"filtering_result\": {",
- "\t\t\"passed_filter_reads\": 9530,",
+ "\t\t\"passed_filter_reads\": 2500,",
"\t\t\"low_quality_reads\": 0,",
"\t\t\"too_many_N_reads\": 0,",
"\t\t\"adapter_dimer_reads\": 0,",
- "\t\t\"too_short_reads\": 4,",
+ "\t\t\"too_short_reads\": 0,",
"\t\t\"too_long_reads\": 0",
"\t},",
"\t\"duplication\": {"
@@ -75,40 +63,40 @@
[
"markdup",
{
- "maxReadLength": 76,
- "minReadLength": 44,
- "meanReadLength": 75,
+ "maxReadLength": 150,
+ "minReadLength": 53,
+ "meanReadLength": 146,
"maxQuality": 60,
"minQuality": 0,
- "meanQuality": 9,
- "readCount": 1101
+ "meanQuality": 41,
+ "readCount": 763
}
],
[
"markdup_log",
[
"LIBRARY\tUNPAIRED_READS_EXAMINED\tREAD_PAIRS_EXAMINED\tSECONDARY_OR_SUPPLEMENTARY_RDS\tUNMAPPED_READS\tUNPAIRED_READ_DUPLICATES\tREAD_PAIR_DUPLICATES\tREAD_PAIR_OPTICAL_DUPLICATES\tPERCENT_DUPLICATION\tESTIMATED_LIBRARY_SIZE",
- "Oct25_PV_10ngR3_F6\t1100\t0\t1\t0\t81\t0\t0\t0.073636\t"
+ "emseq-test1.ds.1\t745\t0\t18\t0\t14\t0\t0\t0.018792\t"
]
],
[
"idxstats",
[
- "chr1\t284940\t1101\t0",
+ "chr1\t284940\t763\t0",
"*\t0\t0\t0"
]
],
[
"flagstats",
[
- "1095 + 6 in total (QC-passed reads + QC-failed reads)",
- "1094 + 6 primary",
- "1 + 0 secondary",
+ "763 + 0 in total (QC-passed reads + QC-failed reads)",
+ "745 + 0 primary",
+ "18 + 0 secondary",
"0 + 0 supplementary",
- "81 + 0 duplicates",
- "81 + 0 primary duplicates",
- "1095 + 6 mapped (100.00% : 100.00%)",
- "1094 + 6 primary mapped (100.00% : 100.00%)",
+ "14 + 0 duplicates",
+ "14 + 0 primary duplicates",
+ "763 + 0 mapped (100.00% : N/A)",
+ "745 + 0 primary mapped (100.00% : N/A)",
"0 + 0 paired in sequencing",
"0 + 0 read1",
"0 + 0 read2",
@@ -123,59 +111,59 @@
"gc_bias",
[
"ACCUMULATION_LEVEL\tREADS_USED\tGC\tWINDOWS\tREAD_STARTS\tMEAN_BASE_QUALITY\tNORMALIZED_COVERAGE\tERROR_BAR_WIDTH\tSAMPLE\tLIBRARY\tREAD_GROUP",
- "All Reads\tALL\t0\t17252\t122\t6\t1.8295\t0.165635\t\t\t",
- "All Reads\tALL\t1\t3503\t37\t6\t2.732585\t0.449234\t\t\t",
- "All Reads\tALL\t2\t5640\t47\t6\t2.155911\t0.314472\t\t\t",
- "All Reads\tALL\t3\t3475\t40\t6\t2.977949\t0.470855\t\t\t",
- "All Reads\tALL\t4\t4275\t45\t5\t2.723256\t0.405959\t\t\t",
- "All Reads\tALL\t5\t3480\t18\t5\t1.338152\t0.315405\t\t\t",
- "All Reads\tALL\t6\t3400\t23\t5\t1.750093\t0.36492\t\t\t",
- "All Reads\tALL\t7\t3235\t19\t6\t1.519468\t0.34859\t\t\t",
- "All Reads\tALL\t8\t3640\t7\t6\t0.497518\t0.188044\t\t\t",
- "All Reads\tALL\t9\t3412\t11\t6\t0.834057\t0.251478\t\t\t",
- "All Reads\tALL\t10\t3608\t12\t6\t0.860452\t0.248391\t\t\t",
- "All Reads\tALL\t11\t3699\t12\t5\t0.839284\t0.24228\t\t\t",
- "All Reads\tALL\t12\t3840\t7\t6\t0.471606\t0.17825\t\t\t",
- "All Reads\tALL\t13\t3874\t8\t7\t0.534248\t0.188885\t\t\t",
- "All Reads\tALL\t14\t3693\t15\t6\t1.05081\t0.271318\t\t\t",
- "All Reads\tALL\t15\t3986\t22\t7\t1.427899\t0.304429\t\t\t",
- "All Reads\tALL\t16\t3911\t17\t7\t1.124536\t0.27274\t\t\t",
- "All Reads\tALL\t17\t3778\t16\t7\t1.095646\t0.273911\t\t\t",
- "All Reads\tALL\t18\t3793\t25\t7\t1.705176\t0.341035\t\t\t",
- "All Reads\tALL\t19\t3698\t30\t7\t2.098778\t0.383183\t\t\t",
- "All Reads\tALL\t20\t3735\t28\t7\t1.939454\t0.366522\t\t\t",
- "All Reads\tALL\t21\t3759\t34\t5\t2.340015\t0.401309\t\t\t",
- "All Reads\tALL\t22\t3461\t35\t6\t2.616246\t0.442226\t\t\t",
- "All Reads\tALL\t23\t3475\t41\t7\t3.052398\t0.476705\t\t\t",
- "All Reads\tALL\t24\t3393\t62\t7\t4.727374\t0.600377\t\t\t",
- "All Reads\tALL\t25\t3365\t52\t7\t3.997886\t0.554407\t\t\t",
- "All Reads\tALL\t26\t3200\t43\t6\t3.476407\t0.530147\t\t\t",
- "All Reads\tALL\t27\t2988\t38\t8\t3.290146\t0.533732\t\t\t",
- "All Reads\tALL\t28\t2852\t35\t6\t3.174904\t0.536657\t\t\t",
- "All Reads\tALL\t29\t2805\t29\t8\t2.674713\t0.496682\t\t\t",
- "All Reads\tALL\t30\t2833\t10\t5\t0.913199\t0.288779\t\t\t",
- "All Reads\tALL\t31\t2731\t23\t7\t2.178805\t0.454312\t\t\t",
- "All Reads\tALL\t32\t2760\t25\t8\t2.343382\t0.468676\t\t\t",
- "All Reads\tALL\t33\t2776\t16\t6\t1.49112\t0.37278\t\t\t",
- "All Reads\tALL\t34\t2475\t15\t5\t1.567935\t0.404839\t\t\t",
- "All Reads\tALL\t35\t2672\t14\t6\t1.355513\t0.362276\t\t\t",
- "All Reads\tALL\t36\t2796\t7\t8\t0.647699\t0.244807\t\t\t",
- "All Reads\tALL\t37\t2850\t9\t11\t0.816977\t0.272326\t\t\t",
- "All Reads\tALL\t38\t2826\t11\t7\t1.007007\t0.303624\t\t\t",
- "All Reads\tALL\t39\t3054\t4\t10\t0.338847\t0.169423\t\t\t",
- "All Reads\tALL\t40\t3449\t6\t8\t0.45006\t0.183736\t\t\t",
- "All Reads\tALL\t41\t4012\t9\t5\t0.580355\t0.193452\t\t\t",
- "All Reads\tALL\t42\t4971\t7\t5\t0.364306\t0.137695\t\t\t",
- "All Reads\tALL\t43\t5630\t5\t6\t0.22976\t0.102752\t\t\t",
- "All Reads\tALL\t44\t6409\t2\t11\t0.080733\t0.057087\t\t\t",
- "All Reads\tALL\t45\t7297\t2\t8\t0.070908\t0.05014\t\t\t",
- "All Reads\tALL\t46\t8146\t2\t10\t0.063518\t0.044914\t\t\t",
- "All Reads\tALL\t47\t8876\t1\t8\t0.029147\t0.029147\t\t\t",
+ "All Reads\tALL\t0\t17252\t5\t8\t0.108195\t0.048386\t\t\t",
+ "All Reads\tALL\t1\t3503\t2\t10\t0.21314\t0.150713\t\t\t",
+ "All Reads\tALL\t2\t5640\t2\t9\t0.132381\t0.093608\t\t\t",
+ "All Reads\tALL\t3\t3475\t0\t0\t0\t0\t\t\t",
+ "All Reads\tALL\t4\t4275\t2\t12\t0.17465\t0.123496\t\t\t",
+ "All Reads\tALL\t5\t3480\t2\t0\t0.214549\t0.151709\t\t\t",
+ "All Reads\tALL\t6\t3400\t1\t0\t0.109798\t0.109798\t\t\t",
+ "All Reads\tALL\t7\t3235\t3\t11\t0.346196\t0.199876\t\t\t",
+ "All Reads\tALL\t8\t3640\t7\t30\t0.717913\t0.271345\t\t\t",
+ "All Reads\tALL\t9\t3412\t6\t17\t0.656473\t0.268004\t\t\t",
+ "All Reads\tALL\t10\t3608\t4\t28\t0.413874\t0.206937\t\t\t",
+ "All Reads\tALL\t11\t3699\t15\t33\t1.513847\t0.390873\t\t\t",
+ "All Reads\tALL\t12\t3840\t20\t20\t1.944347\t0.434769\t\t\t",
+ "All Reads\tALL\t13\t3874\t25\t17\t2.409103\t0.481821\t\t\t",
+ "All Reads\tALL\t14\t3693\t23\t16\t2.325003\t0.484797\t\t\t",
+ "All Reads\tALL\t15\t3986\t38\t19\t3.558945\t0.577337\t\t\t",
+ "All Reads\tALL\t16\t3911\t25\t14\t2.386311\t0.477262\t\t\t",
+ "All Reads\tALL\t17\t3778\t18\t14\t1.778629\t0.419227\t\t\t",
+ "All Reads\tALL\t18\t3793\t36\t16\t3.543191\t0.590532\t\t\t",
+ "All Reads\tALL\t19\t3698\t38\t16\t3.836115\t0.6223\t\t\t",
+ "All Reads\tALL\t20\t3735\t37\t14\t3.698163\t0.607974\t\t\t",
+ "All Reads\tALL\t21\t3759\t40\t14\t3.972488\t0.628105\t\t\t",
+ "All Reads\tALL\t22\t3461\t31\t14\t3.343759\t0.600557\t\t\t",
+ "All Reads\tALL\t23\t3475\t31\t13\t3.330288\t0.598137\t\t\t",
+ "All Reads\tALL\t24\t3393\t27\t13\t2.970673\t0.571706\t\t\t",
+ "All Reads\tALL\t25\t3365\t44\t12\t4.881379\t0.735896\t\t\t",
+ "All Reads\tALL\t26\t3200\t27\t12\t3.149841\t0.606187\t\t\t",
+ "All Reads\tALL\t27\t2988\t33\t13\t4.122952\t0.717714\t\t\t",
+ "All Reads\tALL\t28\t2852\t37\t12\t4.843141\t0.796207\t\t\t",
+ "All Reads\tALL\t29\t2805\t38\t13\t5.057381\t0.820415\t\t\t",
+ "All Reads\tALL\t30\t2833\t21\t12\t2.767245\t0.603862\t\t\t",
+ "All Reads\tALL\t31\t2731\t19\t10\t2.597208\t0.59584\t\t\t",
+ "All Reads\tALL\t32\t2760\t18\t11\t2.43466\t0.573855\t\t\t",
+ "All Reads\tALL\t33\t2776\t23\t13\t3.093024\t0.64494\t\t\t",
+ "All Reads\tALL\t34\t2475\t12\t14\t1.81001\t0.522505\t\t\t",
+ "All Reads\tALL\t35\t2672\t8\t13\t1.117708\t0.39517\t\t\t",
+ "All Reads\tALL\t36\t2796\t6\t12\t0.801104\t0.327049\t\t\t",
+ "All Reads\tALL\t37\t2850\t13\t11\t1.702838\t0.472282\t\t\t",
+ "All Reads\tALL\t38\t2826\t5\t12\t0.6605\t0.295385\t\t\t",
+ "All Reads\tALL\t39\t3054\t4\t13\t0.488952\t0.244476\t\t\t",
+ "All Reads\tALL\t40\t3449\t0\t0\t0\t0\t\t\t",
+ "All Reads\tALL\t41\t4012\t6\t13\t0.558297\t0.227924\t\t\t",
+ "All Reads\tALL\t42\t4971\t5\t12\t0.375492\t0.167925\t\t\t",
+ "All Reads\tALL\t43\t5630\t1\t13\t0.066308\t0.066308\t\t\t",
+ "All Reads\tALL\t44\t6409\t0\t0\t0\t0\t\t\t",
+ "All Reads\tALL\t45\t7297\t1\t12\t0.05116\t0.05116\t\t\t",
+ "All Reads\tALL\t46\t8146\t1\t8\t0.045828\t0.045828\t\t\t",
+ "All Reads\tALL\t47\t8876\t2\t8\t0.084118\t0.05948\t\t\t",
"All Reads\tALL\t48\t9213\t0\t0\t0\t0\t\t\t",
"All Reads\tALL\t49\t9815\t0\t0\t0\t0\t\t\t",
- "All Reads\tALL\t50\t10134\t1\t6\t0.025529\t0.025529\t\t\t",
- "All Reads\tALL\t51\t9913\t1\t3\t0.026098\t0.026098\t\t\t",
- "All Reads\tALL\t52\t9189\t1\t2\t0.028154\t0.028154\t\t\t",
+ "All Reads\tALL\t50\t10134\t1\t22\t0.036838\t0.036838\t\t\t",
+ "All Reads\tALL\t51\t9913\t0\t0\t0\t0\t\t\t",
+ "All Reads\tALL\t52\t9189\t0\t0\t0\t0\t\t\t",
"All Reads\tALL\t53\t8455\t0\t0\t0\t0\t\t\t",
"All Reads\tALL\t54\t7312\t0\t0\t0\t0\t\t\t",
"All Reads\tALL\t55\t5984\t0\t0\t0\t0\t\t\t",
@@ -230,59 +218,59 @@
"gc_bias_groups",
[
"ACCUMULATION_LEVEL\tREADS_USED\tGC\tWINDOWS\tREAD_STARTS\tMEAN_BASE_QUALITY\tNORMALIZED_COVERAGE\tERROR_BAR_WIDTH\tSAMPLE\tLIBRARY\tREAD_GROUP",
- "All Reads\tALL\t0\t17252\t122\t6\t1.8295\t0.165635\t\t\t",
- "All Reads\tALL\t1\t3503\t37\t6\t2.732585\t0.449234\t\t\t",
- "All Reads\tALL\t2\t5640\t47\t6\t2.155911\t0.314472\t\t\t",
- "All Reads\tALL\t3\t3475\t40\t6\t2.977949\t0.470855\t\t\t",
- "All Reads\tALL\t4\t4275\t45\t5\t2.723256\t0.405959\t\t\t",
- "All Reads\tALL\t5\t3480\t18\t5\t1.338152\t0.315405\t\t\t",
- "All Reads\tALL\t6\t3400\t23\t5\t1.750093\t0.36492\t\t\t",
- "All Reads\tALL\t7\t3235\t19\t6\t1.519468\t0.34859\t\t\t",
- "All Reads\tALL\t8\t3640\t7\t6\t0.497518\t0.188044\t\t\t",
- "All Reads\tALL\t9\t3412\t11\t6\t0.834057\t0.251478\t\t\t",
- "All Reads\tALL\t10\t3608\t12\t6\t0.860452\t0.248391\t\t\t",
- "All Reads\tALL\t11\t3699\t12\t5\t0.839284\t0.24228\t\t\t",
- "All Reads\tALL\t12\t3840\t7\t6\t0.471606\t0.17825\t\t\t",
- "All Reads\tALL\t13\t3874\t8\t7\t0.534248\t0.188885\t\t\t",
- "All Reads\tALL\t14\t3693\t15\t6\t1.05081\t0.271318\t\t\t",
- "All Reads\tALL\t15\t3986\t22\t7\t1.427899\t0.304429\t\t\t",
- "All Reads\tALL\t16\t3911\t17\t7\t1.124536\t0.27274\t\t\t",
- "All Reads\tALL\t17\t3778\t16\t7\t1.095646\t0.273911\t\t\t",
- "All Reads\tALL\t18\t3793\t25\t7\t1.705176\t0.341035\t\t\t",
- "All Reads\tALL\t19\t3698\t30\t7\t2.098778\t0.383183\t\t\t",
- "All Reads\tALL\t20\t3735\t28\t7\t1.939454\t0.366522\t\t\t",
- "All Reads\tALL\t21\t3759\t34\t5\t2.340015\t0.401309\t\t\t",
- "All Reads\tALL\t22\t3461\t35\t6\t2.616246\t0.442226\t\t\t",
- "All Reads\tALL\t23\t3475\t41\t7\t3.052398\t0.476705\t\t\t",
- "All Reads\tALL\t24\t3393\t62\t7\t4.727374\t0.600377\t\t\t",
- "All Reads\tALL\t25\t3365\t52\t7\t3.997886\t0.554407\t\t\t",
- "All Reads\tALL\t26\t3200\t43\t6\t3.476407\t0.530147\t\t\t",
- "All Reads\tALL\t27\t2988\t38\t8\t3.290146\t0.533732\t\t\t",
- "All Reads\tALL\t28\t2852\t35\t6\t3.174904\t0.536657\t\t\t",
- "All Reads\tALL\t29\t2805\t29\t8\t2.674713\t0.496682\t\t\t",
- "All Reads\tALL\t30\t2833\t10\t5\t0.913199\t0.288779\t\t\t",
- "All Reads\tALL\t31\t2731\t23\t7\t2.178805\t0.454312\t\t\t",
- "All Reads\tALL\t32\t2760\t25\t8\t2.343382\t0.468676\t\t\t",
- "All Reads\tALL\t33\t2776\t16\t6\t1.49112\t0.37278\t\t\t",
- "All Reads\tALL\t34\t2475\t15\t5\t1.567935\t0.404839\t\t\t",
- "All Reads\tALL\t35\t2672\t14\t6\t1.355513\t0.362276\t\t\t",
- "All Reads\tALL\t36\t2796\t7\t8\t0.647699\t0.244807\t\t\t",
- "All Reads\tALL\t37\t2850\t9\t11\t0.816977\t0.272326\t\t\t",
- "All Reads\tALL\t38\t2826\t11\t7\t1.007007\t0.303624\t\t\t",
- "All Reads\tALL\t39\t3054\t4\t10\t0.338847\t0.169423\t\t\t",
- "All Reads\tALL\t40\t3449\t6\t8\t0.45006\t0.183736\t\t\t",
- "All Reads\tALL\t41\t4012\t9\t5\t0.580355\t0.193452\t\t\t",
- "All Reads\tALL\t42\t4971\t7\t5\t0.364306\t0.137695\t\t\t",
- "All Reads\tALL\t43\t5630\t5\t6\t0.22976\t0.102752\t\t\t",
- "All Reads\tALL\t44\t6409\t2\t11\t0.080733\t0.057087\t\t\t",
- "All Reads\tALL\t45\t7297\t2\t8\t0.070908\t0.05014\t\t\t",
- "All Reads\tALL\t46\t8146\t2\t10\t0.063518\t0.044914\t\t\t",
- "All Reads\tALL\t47\t8876\t1\t8\t0.029147\t0.029147\t\t\t",
+ "All Reads\tALL\t0\t17252\t5\t8\t0.108195\t0.048386\t\t\t",
+ "All Reads\tALL\t1\t3503\t2\t10\t0.21314\t0.150713\t\t\t",
+ "All Reads\tALL\t2\t5640\t2\t9\t0.132381\t0.093608\t\t\t",
+ "All Reads\tALL\t3\t3475\t0\t0\t0\t0\t\t\t",
+ "All Reads\tALL\t4\t4275\t2\t12\t0.17465\t0.123496\t\t\t",
+ "All Reads\tALL\t5\t3480\t2\t0\t0.214549\t0.151709\t\t\t",
+ "All Reads\tALL\t6\t3400\t1\t0\t0.109798\t0.109798\t\t\t",
+ "All Reads\tALL\t7\t3235\t3\t11\t0.346196\t0.199876\t\t\t",
+ "All Reads\tALL\t8\t3640\t7\t30\t0.717913\t0.271345\t\t\t",
+ "All Reads\tALL\t9\t3412\t6\t17\t0.656473\t0.268004\t\t\t",
+ "All Reads\tALL\t10\t3608\t4\t28\t0.413874\t0.206937\t\t\t",
+ "All Reads\tALL\t11\t3699\t15\t33\t1.513847\t0.390873\t\t\t",
+ "All Reads\tALL\t12\t3840\t20\t20\t1.944347\t0.434769\t\t\t",
+ "All Reads\tALL\t13\t3874\t25\t17\t2.409103\t0.481821\t\t\t",
+ "All Reads\tALL\t14\t3693\t23\t16\t2.325003\t0.484797\t\t\t",
+ "All Reads\tALL\t15\t3986\t38\t19\t3.558945\t0.577337\t\t\t",
+ "All Reads\tALL\t16\t3911\t25\t14\t2.386311\t0.477262\t\t\t",
+ "All Reads\tALL\t17\t3778\t18\t14\t1.778629\t0.419227\t\t\t",
+ "All Reads\tALL\t18\t3793\t36\t16\t3.543191\t0.590532\t\t\t",
+ "All Reads\tALL\t19\t3698\t38\t16\t3.836115\t0.6223\t\t\t",
+ "All Reads\tALL\t20\t3735\t37\t14\t3.698163\t0.607974\t\t\t",
+ "All Reads\tALL\t21\t3759\t40\t14\t3.972488\t0.628105\t\t\t",
+ "All Reads\tALL\t22\t3461\t31\t14\t3.343759\t0.600557\t\t\t",
+ "All Reads\tALL\t23\t3475\t31\t13\t3.330288\t0.598137\t\t\t",
+ "All Reads\tALL\t24\t3393\t27\t13\t2.970673\t0.571706\t\t\t",
+ "All Reads\tALL\t25\t3365\t44\t12\t4.881379\t0.735896\t\t\t",
+ "All Reads\tALL\t26\t3200\t27\t12\t3.149841\t0.606187\t\t\t",
+ "All Reads\tALL\t27\t2988\t33\t13\t4.122952\t0.717714\t\t\t",
+ "All Reads\tALL\t28\t2852\t37\t12\t4.843141\t0.796207\t\t\t",
+ "All Reads\tALL\t29\t2805\t38\t13\t5.057381\t0.820415\t\t\t",
+ "All Reads\tALL\t30\t2833\t21\t12\t2.767245\t0.603862\t\t\t",
+ "All Reads\tALL\t31\t2731\t19\t10\t2.597208\t0.59584\t\t\t",
+ "All Reads\tALL\t32\t2760\t18\t11\t2.43466\t0.573855\t\t\t",
+ "All Reads\tALL\t33\t2776\t23\t13\t3.093024\t0.64494\t\t\t",
+ "All Reads\tALL\t34\t2475\t12\t14\t1.81001\t0.522505\t\t\t",
+ "All Reads\tALL\t35\t2672\t8\t13\t1.117708\t0.39517\t\t\t",
+ "All Reads\tALL\t36\t2796\t6\t12\t0.801104\t0.327049\t\t\t",
+ "All Reads\tALL\t37\t2850\t13\t11\t1.702838\t0.472282\t\t\t",
+ "All Reads\tALL\t38\t2826\t5\t12\t0.6605\t0.295385\t\t\t",
+ "All Reads\tALL\t39\t3054\t4\t13\t0.488952\t0.244476\t\t\t",
+ "All Reads\tALL\t40\t3449\t0\t0\t0\t0\t\t\t",
+ "All Reads\tALL\t41\t4012\t6\t13\t0.558297\t0.227924\t\t\t",
+ "All Reads\tALL\t42\t4971\t5\t12\t0.375492\t0.167925\t\t\t",
+ "All Reads\tALL\t43\t5630\t1\t13\t0.066308\t0.066308\t\t\t",
+ "All Reads\tALL\t44\t6409\t0\t0\t0\t0\t\t\t",
+ "All Reads\tALL\t45\t7297\t1\t12\t0.05116\t0.05116\t\t\t",
+ "All Reads\tALL\t46\t8146\t1\t8\t0.045828\t0.045828\t\t\t",
+ "All Reads\tALL\t47\t8876\t2\t8\t0.084118\t0.05948\t\t\t",
"All Reads\tALL\t48\t9213\t0\t0\t0\t0\t\t\t",
"All Reads\tALL\t49\t9815\t0\t0\t0\t0\t\t\t",
- "All Reads\tALL\t50\t10134\t1\t6\t0.025529\t0.025529\t\t\t",
- "All Reads\tALL\t51\t9913\t1\t3\t0.026098\t0.026098\t\t\t",
- "All Reads\tALL\t52\t9189\t1\t2\t0.028154\t0.028154\t\t\t",
+ "All Reads\tALL\t50\t10134\t1\t22\t0.036838\t0.036838\t\t\t",
+ "All Reads\tALL\t51\t9913\t0\t0\t0\t0\t\t\t",
+ "All Reads\tALL\t52\t9189\t0\t0\t0\t0\t\t\t",
"All Reads\tALL\t53\t8455\t0\t0\t0\t0\t\t\t",
"All Reads\tALL\t54\t7312\t0\t0\t0\t0\t\t\t",
"All Reads\tALL\t55\t5984\t0\t0\t0\t0\t\t\t",
@@ -332,59 +320,59 @@
"All Reads\tALL\t99\t0\t0\t0\t0\t0\t\t\t",
"All Reads\tALL\t100\t0\t0\t0\t0\t0\t\t\t",
"ACCUMULATION_LEVEL\tREADS_USED\tGC\tWINDOWS\tREAD_STARTS\tMEAN_BASE_QUALITY\tNORMALIZED_COVERAGE\tERROR_BAR_WIDTH\tSAMPLE\tLIBRARY\tREAD_GROUP",
- "testorg\tALL\t0\t17252\t122\t6\t1.8295\t0.165635\t\t\t",
- "testorg\tALL\t1\t3503\t37\t6\t2.732585\t0.449234\t\t\t",
- "testorg\tALL\t2\t5640\t47\t6\t2.155911\t0.314472\t\t\t",
- "testorg\tALL\t3\t3475\t40\t6\t2.977949\t0.470855\t\t\t",
- "testorg\tALL\t4\t4275\t45\t5\t2.723256\t0.405959\t\t\t",
- "testorg\tALL\t5\t3480\t18\t5\t1.338152\t0.315405\t\t\t",
- "testorg\tALL\t6\t3400\t23\t5\t1.750093\t0.36492\t\t\t",
- "testorg\tALL\t7\t3235\t19\t6\t1.519468\t0.34859\t\t\t",
- "testorg\tALL\t8\t3640\t7\t6\t0.497518\t0.188044\t\t\t",
- "testorg\tALL\t9\t3412\t11\t6\t0.834057\t0.251478\t\t\t",
- "testorg\tALL\t10\t3608\t12\t6\t0.860452\t0.248391\t\t\t",
- "testorg\tALL\t11\t3699\t12\t5\t0.839284\t0.24228\t\t\t",
- "testorg\tALL\t12\t3840\t7\t6\t0.471606\t0.17825\t\t\t",
- "testorg\tALL\t13\t3874\t8\t7\t0.534248\t0.188885\t\t\t",
- "testorg\tALL\t14\t3693\t15\t6\t1.05081\t0.271318\t\t\t",
- "testorg\tALL\t15\t3986\t22\t7\t1.427899\t0.304429\t\t\t",
- "testorg\tALL\t16\t3911\t17\t7\t1.124536\t0.27274\t\t\t",
- "testorg\tALL\t17\t3778\t16\t7\t1.095646\t0.273911\t\t\t",
- "testorg\tALL\t18\t3793\t25\t7\t1.705176\t0.341035\t\t\t",
- "testorg\tALL\t19\t3698\t30\t7\t2.098778\t0.383183\t\t\t",
- "testorg\tALL\t20\t3735\t28\t7\t1.939454\t0.366522\t\t\t",
- "testorg\tALL\t21\t3759\t34\t5\t2.340015\t0.401309\t\t\t",
- "testorg\tALL\t22\t3461\t35\t6\t2.616246\t0.442226\t\t\t",
- "testorg\tALL\t23\t3475\t41\t7\t3.052398\t0.476705\t\t\t",
- "testorg\tALL\t24\t3393\t62\t7\t4.727374\t0.600377\t\t\t",
- "testorg\tALL\t25\t3365\t52\t7\t3.997886\t0.554407\t\t\t",
- "testorg\tALL\t26\t3200\t43\t6\t3.476407\t0.530147\t\t\t",
- "testorg\tALL\t27\t2988\t38\t8\t3.290146\t0.533732\t\t\t",
- "testorg\tALL\t28\t2852\t35\t6\t3.174904\t0.536657\t\t\t",
- "testorg\tALL\t29\t2805\t29\t8\t2.674713\t0.496682\t\t\t",
- "testorg\tALL\t30\t2833\t10\t5\t0.913199\t0.288779\t\t\t",
- "testorg\tALL\t31\t2731\t23\t7\t2.178805\t0.454312\t\t\t",
- "testorg\tALL\t32\t2760\t25\t8\t2.343382\t0.468676\t\t\t",
- "testorg\tALL\t33\t2776\t16\t6\t1.49112\t0.37278\t\t\t",
- "testorg\tALL\t34\t2475\t15\t5\t1.567935\t0.404839\t\t\t",
- "testorg\tALL\t35\t2672\t14\t6\t1.355513\t0.362276\t\t\t",
- "testorg\tALL\t36\t2796\t7\t8\t0.647699\t0.244807\t\t\t",
- "testorg\tALL\t37\t2850\t9\t11\t0.816977\t0.272326\t\t\t",
- "testorg\tALL\t38\t2826\t11\t7\t1.007007\t0.303624\t\t\t",
- "testorg\tALL\t39\t3054\t4\t10\t0.338847\t0.169423\t\t\t",
- "testorg\tALL\t40\t3449\t6\t8\t0.45006\t0.183736\t\t\t",
- "testorg\tALL\t41\t4012\t9\t5\t0.580355\t0.193452\t\t\t",
- "testorg\tALL\t42\t4971\t7\t5\t0.364306\t0.137695\t\t\t",
- "testorg\tALL\t43\t5630\t5\t6\t0.22976\t0.102752\t\t\t",
- "testorg\tALL\t44\t6409\t2\t11\t0.080733\t0.057087\t\t\t",
- "testorg\tALL\t45\t7297\t2\t8\t0.070908\t0.05014\t\t\t",
- "testorg\tALL\t46\t8146\t2\t10\t0.063518\t0.044914\t\t\t",
- "testorg\tALL\t47\t8876\t1\t8\t0.029147\t0.029147\t\t\t",
+ "testorg\tALL\t0\t17252\t5\t8\t0.108195\t0.048386\t\t\t",
+ "testorg\tALL\t1\t3503\t2\t10\t0.21314\t0.150713\t\t\t",
+ "testorg\tALL\t2\t5640\t2\t9\t0.132381\t0.093608\t\t\t",
+ "testorg\tALL\t3\t3475\t0\t0\t0\t0\t\t\t",
+ "testorg\tALL\t4\t4275\t2\t12\t0.17465\t0.123496\t\t\t",
+ "testorg\tALL\t5\t3480\t2\t0\t0.214549\t0.151709\t\t\t",
+ "testorg\tALL\t6\t3400\t1\t0\t0.109798\t0.109798\t\t\t",
+ "testorg\tALL\t7\t3235\t3\t11\t0.346196\t0.199876\t\t\t",
+ "testorg\tALL\t8\t3640\t7\t30\t0.717913\t0.271345\t\t\t",
+ "testorg\tALL\t9\t3412\t6\t17\t0.656473\t0.268004\t\t\t",
+ "testorg\tALL\t10\t3608\t4\t28\t0.413874\t0.206937\t\t\t",
+ "testorg\tALL\t11\t3699\t15\t33\t1.513847\t0.390873\t\t\t",
+ "testorg\tALL\t12\t3840\t20\t20\t1.944347\t0.434769\t\t\t",
+ "testorg\tALL\t13\t3874\t25\t17\t2.409103\t0.481821\t\t\t",
+ "testorg\tALL\t14\t3693\t23\t16\t2.325003\t0.484797\t\t\t",
+ "testorg\tALL\t15\t3986\t38\t19\t3.558945\t0.577337\t\t\t",
+ "testorg\tALL\t16\t3911\t25\t14\t2.386311\t0.477262\t\t\t",
+ "testorg\tALL\t17\t3778\t18\t14\t1.778629\t0.419227\t\t\t",
+ "testorg\tALL\t18\t3793\t36\t16\t3.543191\t0.590532\t\t\t",
+ "testorg\tALL\t19\t3698\t38\t16\t3.836115\t0.6223\t\t\t",
+ "testorg\tALL\t20\t3735\t37\t14\t3.698163\t0.607974\t\t\t",
+ "testorg\tALL\t21\t3759\t40\t14\t3.972488\t0.628105\t\t\t",
+ "testorg\tALL\t22\t3461\t31\t14\t3.343759\t0.600557\t\t\t",
+ "testorg\tALL\t23\t3475\t31\t13\t3.330288\t0.598137\t\t\t",
+ "testorg\tALL\t24\t3393\t27\t13\t2.970673\t0.571706\t\t\t",
+ "testorg\tALL\t25\t3365\t44\t12\t4.881379\t0.735896\t\t\t",
+ "testorg\tALL\t26\t3200\t27\t12\t3.149841\t0.606187\t\t\t",
+ "testorg\tALL\t27\t2988\t33\t13\t4.122952\t0.717714\t\t\t",
+ "testorg\tALL\t28\t2852\t37\t12\t4.843141\t0.796207\t\t\t",
+ "testorg\tALL\t29\t2805\t38\t13\t5.057381\t0.820415\t\t\t",
+ "testorg\tALL\t30\t2833\t21\t12\t2.767245\t0.603862\t\t\t",
+ "testorg\tALL\t31\t2731\t19\t10\t2.597208\t0.59584\t\t\t",
+ "testorg\tALL\t32\t2760\t18\t11\t2.43466\t0.573855\t\t\t",
+ "testorg\tALL\t33\t2776\t23\t13\t3.093024\t0.64494\t\t\t",
+ "testorg\tALL\t34\t2475\t12\t14\t1.81001\t0.522505\t\t\t",
+ "testorg\tALL\t35\t2672\t8\t13\t1.117708\t0.39517\t\t\t",
+ "testorg\tALL\t36\t2796\t6\t12\t0.801104\t0.327049\t\t\t",
+ "testorg\tALL\t37\t2850\t13\t11\t1.702838\t0.472282\t\t\t",
+ "testorg\tALL\t38\t2826\t5\t12\t0.6605\t0.295385\t\t\t",
+ "testorg\tALL\t39\t3054\t4\t13\t0.488952\t0.244476\t\t\t",
+ "testorg\tALL\t40\t3449\t0\t0\t0\t0\t\t\t",
+ "testorg\tALL\t41\t4012\t6\t13\t0.558297\t0.227924\t\t\t",
+ "testorg\tALL\t42\t4971\t5\t12\t0.375492\t0.167925\t\t\t",
+ "testorg\tALL\t43\t5630\t1\t13\t0.066308\t0.066308\t\t\t",
+ "testorg\tALL\t44\t6409\t0\t0\t0\t0\t\t\t",
+ "testorg\tALL\t45\t7297\t1\t12\t0.05116\t0.05116\t\t\t",
+ "testorg\tALL\t46\t8146\t1\t8\t0.045828\t0.045828\t\t\t",
+ "testorg\tALL\t47\t8876\t2\t8\t0.084118\t0.05948\t\t\t",
"testorg\tALL\t48\t9213\t0\t0\t0\t0\t\t\t",
"testorg\tALL\t49\t9815\t0\t0\t0\t0\t\t\t",
- "testorg\tALL\t50\t10134\t1\t6\t0.025529\t0.025529\t\t\t",
- "testorg\tALL\t51\t9913\t1\t3\t0.026098\t0.026098\t\t\t",
- "testorg\tALL\t52\t9189\t1\t2\t0.028154\t0.028154\t\t\t",
+ "testorg\tALL\t50\t10134\t1\t22\t0.036838\t0.036838\t\t\t",
+ "testorg\tALL\t51\t9913\t0\t0\t0\t0\t\t\t",
+ "testorg\tALL\t52\t9189\t0\t0\t0\t0\t\t\t",
"testorg\tALL\t53\t8455\t0\t0\t0\t0\t\t\t",
"testorg\tALL\t54\t7312\t0\t0\t0\t0\t\t\t",
"testorg\tALL\t55\t5984\t0\t0\t0\t0\t\t\t",
@@ -439,18 +427,18 @@
"alignment_metrics",
[
"CATEGORY\tTOTAL_READS\tPF_READS\tPCT_PF_READS\tPF_NOISE_READS\tPF_READS_ALIGNED\tPCT_PF_READS_ALIGNED\tPF_ALIGNED_BASES\tPF_HQ_ALIGNED_READS\tPF_HQ_ALIGNED_BASES\tPF_HQ_ALIGNED_Q20_BASES\tPF_HQ_MEDIAN_MISMATCHES\tPF_MISMATCH_RATE\tPF_HQ_ERROR_RATE\tPF_INDEL_RATE\tMEAN_READ_LENGTH\tSD_READ_LENGTH\tMEDIAN_READ_LENGTH\tMAD_READ_LENGTH\tMIN_READ_LENGTH\tMAX_READ_LENGTH\tMEAN_ALIGNED_READ_LENGTH\tREADS_ALIGNED_IN_PAIRS\tPCT_READS_ALIGNED_IN_PAIRS\tPF_READS_IMPROPER_PAIRS\tPCT_PF_READS_IMPROPER_PAIRS\tBAD_CYCLES\tSTRAND_BALANCE\tPCT_CHIMERAS\tPCT_ADAPTER\tPCT_SOFTCLIP\tPCT_HARDCLIP\tAVG_POS_3PRIME_SOFTCLIP_LENGTH\tSAMPLE\tLIBRARY\tREAD_GROUP",
- "UNPAIRED\t1100\t1094\t0.994545\t0\t1094\t1\t80799\t224\t16598\t15805\t0\t0.205196\t0.161755\t0.004616\t75.754113\t2.037807\t76\t0\t44\t76\t74.196527\t0\t0\t0\t0\t0\t0.674589\t0.004464\t0\t0.020561\t0\t18.139535\t\t\t",
+ "UNPAIRED\t745\t745\t1\t0\t745\t1\t99162\t537\t76242\t75002\t0\t0.034304\t0.014897\t0.002219\t148.559732\t6.956237\t150\t0\t71\t150\t133.465772\t0\t0\t0\t0\t0\t0.989262\t0.018622\t0\t0.101602\t0\t49.564103\t\t\t",
"## HISTOGRAM\tjava.lang.Integer",
"READ_LENGTH\tUNPAIRED_TOTAL_LENGTH_COUNT\tUNPAIRED_ALIGNED_LENGTH_COUNT"
]
],
[
"methyldackel_extract",
- "91eac7636f2e617927f190e3e884b8c9"
+ "55ab0743f01e4d66921bacd7dd3ef411"
],
[
"mbias",
- "824e46917dfa852f1f3ed83571008eef"
+ "20c46a85d89d9fa53ed671a1372a7299"
],
[
"nonconverted",
@@ -461,15 +449,17 @@
[
"nonconverted_combined",
[
- "emseq-test1\tchr1\t0"
+ "emseq-test1.ds.1\tchr1\t0"
]
],
[
"positional_summary",
[
"methylkit_file\tchr\ttarget_length\tposition\tcontext\tmean_methylation\tn_loci\tn_measurements",
- "emseq-test1\tchr1\t182\t178\tCG\t0\t1\t1",
- "emseq-test1\tchr1\t204\t189\tCG\t0\t1\t1"
+ "emseq-test1.ds.1\tchr1\t208\t110\tCG\t100\t1\t1",
+ "emseq-test1.ds.1\tchr1\t204\t189\tCG\t33.3333\t1\t1",
+ "emseq-test1.ds.1\tchr1\t151\t142\tCG\t100\t1\t1",
+ "emseq-test1.ds.1\tchr1\t182\t178\tCG\t33.3333\t1\t1"
]
],
[
@@ -479,17 +469,13 @@
[
"region_summary",
[
- "library\ttarget_locus\ttarget_name\tcontext\tmean_methylation",
- "emseq-test2\tchr1:140839-141043\tStemLoop_140889_140992_2mm_22C_0CG\tCG\t0",
- "emseq-test2\tchr1:140850-141032\tStemLoop_140900_140981_0mm_29C_1CG\tCG\t0"
+ "library\ttarget_locus\ttarget_name\tcontext\tmean_methylation"
]
],
[
"methylkit_intersections",
[
- "methylkit_file\tchr\tstart\tend\tcontext\tmethylation\ttarget_locus\ttarget_name",
- "emseq-test2\tchr1\t141027\t141028\tCG\t0\tchr1:140840-141043\tStemLoop_140889_140992_2mm_22C_0CG",
- "emseq-test2\tchr1\t141027\t141028\tCG\t0\tchr1:140851-141032\tStemLoop_140900_140981_0mm_29C_1CG"
+ "methylkit_file\tchr\tstart\tend\tcontext\tmethylation\ttarget_locus\ttarget_name"
]
],
[
@@ -503,37 +489,37 @@
[
"ngs_agg",
[
- "--bam emseq-test1.md.bam ",
- "--bai emseq-test1.md.bai ",
- "--metadata_bam_file emseq-test1.bam ",
- "--fastp emseq-test1.fastp.json ",
- "--aln emseq-test1.alignment_summary_metrics.txt ",
- "--gc emseq-test1.gc_metrics.combined.tsv ",
- "--dup emseq-test1.markdups_log ",
- "--idx_stats emseq-test1.idxstat ",
- "--flagstat emseq-test1.flagstat ",
- "--fastqc emseq-test1.md_fastqc.zip ",
- "--nonconverted_read_counts emseq-test1.nonconverted_counts.for_agg.tsv ",
- "--tasmanian emseq-test1.tasmanian.csv ",
- "--combined_mbias_records emseq-test1.combined_mbias.tsv ",
- "--fgbio_switchbacks emseq-test1.switchbacks.summary.txt ",
+ "--bam emseq-test1.ds.1.md.bam ",
+ "--bai emseq-test1.ds.1.md.bai ",
+ "--metadata_bam_file emseq-test1.ds.1.bam ",
+ "--fastp emseq-test1.ds.1.fastp.json ",
+ "--aln emseq-test1.ds.1.alignment_summary_metrics.txt ",
+ "--gc emseq-test1.ds.1.gc_metrics.combined.tsv ",
+ "--dup emseq-test1.ds.1.markdups_log ",
+ "--idx_stats emseq-test1.ds.1.idxstat ",
+ "--flagstat emseq-test1.ds.1.flagstat ",
+ "--fastqc emseq-test1.ds.1.md_fastqc.zip ",
+ "--nonconverted_read_counts emseq-test1.ds.1.nonconverted_counts.for_agg.tsv ",
+ "--tasmanian emseq-test1.ds.1.tasmanian.csv ",
+ "--combined_mbias_records emseq-test1.ds.1.combined_mbias.tsv ",
+ "--fgbio_switchbacks emseq-test1.ds.1.switchbacks.summary.txt ",
"--genome_contigs contig_groups.tsv",
"--workflow EM-seq"
]
]
],
- "timestamp": "2026-08-28T16:51:33.805201239",
+ "timestamp": "2026-09-14T18:18:06.511679526",
"meta": {
"nf-test": "0.9.5",
- "nextflow": "24.10.5"
+ "nextflow": "25.10.4"
}
},
"EM-seq workflow uBam": {
"content": [
{
- "tasksCount": 53,
+ "tasksCount": 49,
"tasksFailed": 0,
- "tasksSucceeded": 53
+ "tasksSucceeded": 49
},
[
"bwameth_file_1",
@@ -567,7 +553,7 @@
"fastp",
[
"\t\"summary\": {",
- "\t\t\"fastp_version\": \"1.3.6\",",
+ "\t\t\"fastp_version\": \"0.1.0\",",
"\t\t\"sequencing\": \"paired end (76 cycles + 76 cycles)\",",
"\t\t\"before_filtering\": {",
"\t\t\t\"total_reads\": 9534,",
@@ -578,18 +564,18 @@
"\t\t\t\"q30_rate\": 0.913898,",
"\t\t\t\"read1_mean_length\": 76,",
"\t\t\t\"read2_mean_length\": 76,",
- "\t\t\t\"gc_content\": 0.218667",
+ "\t\t\t\"gc_content\": 0.218668",
"\t\t},",
"\t\t\"after_filtering\": {",
"\t\t\t\"total_reads\": 9526,",
- "\t\t\t\"total_bases\": 719151,",
- "\t\t\t\"q20_bases\": 676526,",
- "\t\t\t\"q30_bases\": 657902,",
- "\t\t\t\"q20_rate\": 0.940729,",
- "\t\t\t\"q30_rate\": 0.914832,",
+ "\t\t\t\"total_bases\": 719317,",
+ "\t\t\t\"q20_bases\": 676675,",
+ "\t\t\t\"q30_bases\": 658048,",
+ "\t\t\t\"q20_rate\": 0.940719,",
+ "\t\t\t\"q30_rate\": 0.914823,",
"\t\t\t\"read1_mean_length\": 75,",
"\t\t\t\"read2_mean_length\": 75,",
- "\t\t\t\"gc_content\": 0.216787",
+ "\t\t\t\"gc_content\": 0.216795",
"\t\t}",
"\t},",
"\t\"filtering_result\": {",
@@ -639,20 +625,20 @@
[
"flagstats",
[
- "1215 + 584 in total (QC-passed reads + QC-failed reads)",
- "1214 + 584 primary",
+ "1799 + 0 in total (QC-passed reads + QC-failed reads)",
+ "1798 + 0 primary",
"1 + 0 secondary",
"0 + 0 supplementary",
- "22 + 2 duplicates",
- "22 + 2 primary duplicates",
- "956 + 579 mapped (78.68% : 99.14%)",
- "955 + 579 primary mapped (78.67% : 99.14%)",
- "1214 + 584 paired in sequencing",
- "607 + 292 read1",
- "607 + 292 read2",
- "674 + 0 properly paired (55.52% : 0.00%)",
- "696 + 574 with itself and mate mapped",
- "259 + 5 singletons (21.33% : 0.86%)",
+ "24 + 0 duplicates",
+ "24 + 0 primary duplicates",
+ "1535 + 0 mapped (85.33% : N/A)",
+ "1534 + 0 primary mapped (85.32% : N/A)",
+ "1798 + 0 paired in sequencing",
+ "899 + 0 read1",
+ "899 + 0 read2",
+ "674 + 0 properly paired (37.49% : N/A)",
+ "1270 + 0 with itself and mate mapped",
+ "264 + 0 singletons (14.68% : N/A)",
"0 + 0 with mate mapped to a different chr",
"0 + 0 with mate mapped to a different chr (mapQ>=5)"
]
@@ -977,9 +963,9 @@
"alignment_metrics",
[
"CATEGORY\tTOTAL_READS\tPF_READS\tPCT_PF_READS\tPF_NOISE_READS\tPF_READS_ALIGNED\tPCT_PF_READS_ALIGNED\tPF_ALIGNED_BASES\tPF_HQ_ALIGNED_READS\tPF_HQ_ALIGNED_BASES\tPF_HQ_ALIGNED_Q20_BASES\tPF_HQ_MEDIAN_MISMATCHES\tPF_MISMATCH_RATE\tPF_HQ_ERROR_RATE\tPF_INDEL_RATE\tMEAN_READ_LENGTH\tSD_READ_LENGTH\tMEDIAN_READ_LENGTH\tMAD_READ_LENGTH\tMIN_READ_LENGTH\tMAX_READ_LENGTH\tMEAN_ALIGNED_READ_LENGTH\tREADS_ALIGNED_IN_PAIRS\tPCT_READS_ALIGNED_IN_PAIRS\tPF_READS_IMPROPER_PAIRS\tPCT_PF_READS_IMPROPER_PAIRS\tBAD_CYCLES\tSTRAND_BALANCE\tPCT_CHIMERAS\tPCT_ADAPTER\tPCT_SOFTCLIP\tPCT_HARDCLIP\tAVG_POS_3PRIME_SOFTCLIP_LENGTH\tSAMPLE\tLIBRARY\tREAD_GROUP",
- "FIRST_OF_PAIR\t899\t607\t0.675195\t0\t493\t0.812191\t32309\t302\t19684\t18772\t3\t0.103312\t0.098954\t0.004364\t74.663921\t5.91042\t76\t0\t31\t76\t53.443163\t348\t0.705882\t156\t0.31643\t0\t0.89858\t0.010101\t0\t0.093312\t0\t15.835294\t\t\t",
- "SECOND_OF_PAIR\t899\t607\t0.675195\t0\t462\t0.76112\t30277\t299\t19999\t18469\t3\t0.102474\t0.09557\t0.004096\t74.710049\t5.864669\t76\t0\t31\t76\t50.116969\t348\t0.753247\t125\t0.270563\t0\t0.112554\t0.010453\t0\t0.086176\t0\t14.56701\t\t\t",
- "PAIR\t1798\t1214\t0.675195\t0\t955\t0.786656\t62586\t601\t39683\t37241\t3\t0.102909\t0.097258\t0.004234\t74.686985\t5.885207\t76\t0\t31\t76\t51.780066\t696\t0.728796\t281\t0.294241\t0\t0.518325\t0.010274\t0\t0.089743\t0\t15.159341\t\t\t"
+ "FIRST_OF_PAIR\t899\t899\t1\t0\t781\t0.868743\t42522\t344\t22297\t21272\t0\t0.109413\t0.102292\t0.005362\t74.83426\t5.220772\t76\t0\t31\t76\t47.575083\t635\t0.81306\t444\t0.568502\t0\t0.806658\t0.010101\t0\t0.231137\t0\t23.036866\t\t\t",
+ "SECOND_OF_PAIR\t899\t899\t1\t3\t753\t0.837597\t40929\t343\t22862\t21179\t0\t0.110193\t0.097406\t0.004984\t74.865406\t5.184858\t76\t0\t31\t76\t45.799778\t635\t0.843293\t416\t0.552457\t0\t0.203187\t0.010453\t0\t0.223375\t0\t20.209016\t\t\t",
+ "PAIR\t1798\t1798\t1\t3\t1534\t0.85317\t83451\t687\t45159\t42451\t0\t0.109795\t0.09983\t0.005177\t74.849833\t5.201422\t76\t0\t31\t76\t46.68743\t1270\t0.827901\t860\t0.560626\t0\t0.51043\t0.010274\t0\t0.227255\t0\t21.54013\t\t\t"
]
],
[
@@ -1094,10 +1080,10 @@
]
]
],
- "timestamp": "2026-08-28T16:51:07.761902237",
+ "timestamp": "2026-09-14T18:16:48.752140047",
"meta": {
"nf-test": "0.9.5",
- "nextflow": "24.10.5"
+ "nextflow": "25.10.4"
}
}
}
\ No newline at end of file
]