chore: post-release cleanup for v1.2.0

CHANGELOG.md

@@ -1,3 +1,5 @@
+## ASPEN development version
+
 ## ASPEN 1.2.0
 
 - Add `hs1_chrR` as a supported reference genome (T2T-CHM13 + chrR rDNA unit from [Paralkar lab](https://github.com/vikramparalkar/rDNA-Mapping-Genomes)). (#117, @kopardev)

VERSION

@@ -1 +1 @@
-1.2.0
+1.2.0-dev

docs/deployment.md

@@ -31,13 +31,13 @@ ASPEN requires a sample manifest file (`samples.tsv`) to identify and organize y
 - `path_to_R2_fastq`: Absolute path to the Read 2 FASTQ file (required for paired-end data).
 
 !!! note
-    Symlinks for R1 and R2 files will be created in the results directory, named as `<replicateName>.R1.fastq.gz` and `<replicateName>.R2.fastq.gz`, respectively. Therefore, original filenames do not need to be altered.
+Symlinks for R1 and R2 files will be created in the results directory, named as `<replicateName>.R1.fastq.gz` and `<replicateName>.R2.fastq.gz`, respectively. Therefore, original filenames do not need to be altered.
 
 !!! note
-    The `replicateName` is used as a prefix for individual peak calls, while the `sampleName` serves as a prefix for consensus peak calls.
+The `replicateName` is used as a prefix for individual peak calls, while the `sampleName` serves as a prefix for consensus peak calls.
 
 !!! warning "Biological vs. technical replicates"
-    ASPEN expects **one row per biological replicate**. If you sequenced the same sample across multiple lanes or sequencing runs (technical replicates), you must **concatenate those FASTQ files into a single file** before creating your manifest — ASPEN does not merge lanes internally.
+ASPEN expects **one row per biological replicate**. If you sequenced the same sample across multiple lanes or sequencing runs (technical replicates), you must **concatenate those FASTQ files into a single file** before creating your manifest — ASPEN does not merge lanes internally.
 
     | Replicate type | Definition | What to do |
     |---|---|---|
@@ -53,7 +53,7 @@ ASPEN requires a sample manifest file (`samples.tsv`) to identify and organize y
     DESeq2 (used in `diffatac`) requires **at least 2 biological replicates per group**. Technical replicates do not count as biological replicates and will not satisfy this requirement.
 
 !!! note
-    For differential ATAC analysis, create a `contrasts.tsv` file with two columns (Group1 and Group2 ... aka Sample1 and Sample2, without headers) and place it in the output directory after initialization. Ensure each group/sample in the contrast has at least two biological replicates, as DESeq2 requires this for accurate contrast calculations.
+For differential ATAC analysis, create a `contrasts.tsv` file with two columns (Group1 and Group2 ... aka Sample1 and Sample2, without headers) and place it in the output directory after initialization. Ensure each group/sample in the contrast has at least two biological replicates, as DESeq2 requires this for accurate contrast calculations.
 
 ## 🏃 Running the ASPEN Pipeline
 

docs/limitations.md

@@ -8,14 +8,14 @@
 
 - **Genomes supported**: Genomes supported is limited to:
 
-| Genome Assembly | Organism        | Scientific Name  |
-| --------------- | --------------- | ---------------- |
-| hg38            | Human           | _Homo sapiens_   |
-| hg19            | Human           | _Homo sapiens_   |
-| mm10            | Mouse           | _Mus musculus_   |
-| mmul10          | Rhesus Monkey   | _Macaca mulatta_ |
-| bosTau9         | Domestic Cattle | _Bos taurus_     |
-| hs1             | Human           | _Homo sapiens_ (T2T-CHM13) |
+| Genome Assembly | Organism        | Scientific Name                                             |
+| --------------- | --------------- | ----------------------------------------------------------- |
+| hg38            | Human           | _Homo sapiens_                                              |
+| hg19            | Human           | _Homo sapiens_                                              |
+| mm10            | Mouse           | _Mus musculus_                                              |
+| mmul10          | Rhesus Monkey   | _Macaca mulatta_                                            |
+| bosTau9         | Domestic Cattle | _Bos taurus_                                                |
+| hs1             | Human           | _Homo sapiens_ (T2T-CHM13)                                  |
 | hs1_chrR        | Human           | _Homo sapiens_ (T2T-CHM13 + chrR rDNA unit; see note below) |
 
     !!! tip "Use `hs1_chrR` for ribosomal DNA chromatin accessibility studies"

docs/outputs.md

@@ -138,7 +138,7 @@ important for interpreting output files and configuring the pipeline correctly.
 
 **Round 1 — Per-sample consensus** (`*.macs2.consensus.bed` / `*.genrich.consensus.bed`)
 
-> *"Which peaks are reproducible across biological replicates of the same sample?"*
+> _"Which peaks are reproducible across biological replicates of the same sample?"_
 
 1. All replicate tagAlign files for a sample are **pooled** and passed to MACS2/Genrich together → produces a large set of candidate peaks from the pooled data.
 2. Each candidate peak is checked for overlap with peaks called in each **individual replicate**.
@@ -152,7 +152,7 @@ replicate 3 peaks ─┘                    (≥ min_replicates)
 
 **Round 2 — ROI consensus** (`ROI.macs2.bed` / `ROI.genrich.bed`)
 
-> *"Across ALL samples, what is the unified set of fixed-width windows for differential accessibility analysis?"*
+> _"Across ALL samples, what is the unified set of fixed-width windows for differential accessibility analysis?"_
 
 1. Per-sample consensus peaks are converted to **fixed-width windows** (default: 500 bp, centered on the peak summit) using the method from [Corces et al. 2018](https://doi.org/10.1038/nmeth.4396). Window width is controlled by `fixed_width` in `config.yaml`.
 2. Fixed-width peaks from all samples are **merged** → `ROI.macs2.bed` — the master set of regions used for DESeq2 read counting and differential accessibility analysis.
@@ -165,11 +165,12 @@ sample3.consensus.bed ─► fixed-width peaks ─┘
 ```
 
 !!! tip "Config knobs that control consensus"
-    | Parameter | Default | Effect |
-    |---|---|---|
-    | `consensus_min_replicates` | `1` | Min. replicates a peak must appear in to be retained in per-sample consensus |
-    | `consensus_min_spm` | `5` | Min. signal-per-million reads threshold for a peak to be included |
-    | `fixed_width` | `500` | Width (bp) of fixed-width peaks used to build the ROI set |
+
+| Parameter                  | Default | Effect                                                                       |
+| -------------------------- | ------- | ---------------------------------------------------------------------------- |
+| `consensus_min_replicates` | `1`     | Min. replicates a peak must appear in to be retained in per-sample consensus |
+| `consensus_min_spm`        | `5`     | Min. signal-per-million reads threshold for a peak to be included            |
+| `fixed_width`              | `500`   | Width (bp) of fixed-width peaks used to build the ROI set                    |
 
 #### Peak Annotation folder
 

workflow/scripts/ccbr_annotate_bed.R

@@ -118,7 +118,9 @@ if (args$genome == "bosTau9") {
   tdb <- TxDb.Btaurus.UCSC.bosTau9.refGene
 }
 if (args$genome %in% c("hs1", "hs1_chrR")) {
-  tdb <- AnnotationDbi::loadDb("/opt2/annotation/TxDb.Hsapiens.NCBI.T2T.CHM13v2.0.sqlite")
+  tdb <- AnnotationDbi::loadDb(
+    "/opt2/annotation/TxDb.Hsapiens.NCBI.T2T.CHM13v2.0.sqlite"
+  )
 }
 
 

workflow/scripts/ccbr_annotate_peaks.R

@@ -118,7 +118,9 @@ if (args$genome == "bosTau9") {
   tdb <- TxDb.Btaurus.UCSC.bosTau9.refGene
 }
 if (args$genome %in% c("hs1", "hs1_chrR")) {
-  tdb <- AnnotationDbi::loadDb("/opt2/annotation/TxDb.Hsapiens.NCBI.T2T.CHM13v2.0.sqlite")
+  tdb <- AnnotationDbi::loadDb(
+    "/opt2/annotation/TxDb.Hsapiens.NCBI.T2T.CHM13v2.0.sqlite"
+  )
 }
 
 

workflow/scripts/ccbr_atac_bam2tn5bed.py

@@ -237,6 +237,4 @@ def extract_fragments(input_bam, output_tn5, output_reads, threads, chrom_sizes)
     )
     args = parser.parse_args()
     genome_sizes = parse_genome_sizes(args.genomefile)
-    extract_fragments(
-        args.bam, args.tn5bed, args.readsbed, args.ncpus, genome_sizes
-    )
+    extract_fragments(args.bam, args.tn5bed, args.readsbed, args.ncpus, genome_sizes)

workflow/scripts/ccbr_bam_filter_by_mapq.py

@@ -42,4 +42,4 @@
             continue
         pairedreads.write(read)
 samfile.close()
-pairedreads.close()
+pairedreads.close()