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Merge pull request #583 from nf-core/fix-publishing
Fix rrbs and skip_dedup publishing
2 parents 7f30dbf + e56eb61 commit 04f4e35

18 files changed

+586
-240
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‎CHANGELOG.md‎

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@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- 🐛 Fix error in `picard_bedtointervallist.config` [#566](https://github.com/nf-core/methylseq/pull/566)
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- 🐛 Fix error when using --aligner bwameth with samtools sort, the output bams will be labeled with prefix "${meta.id}.deduplicated.sorted" and published in the deduplication folder [#580](https://github.com/nf-core/methylseq/pull/581)
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- 🐛 Fix publishing of bam files in the alignments folder when using --skip_deduplication or --rrbs [#579](https://github.com/nf-core/methylseq/pull/583)
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- 🔧 Update Bismark to v0.25.1 [#569](https://github.com/nf-core/methylseq/pull/569)
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- 🔧 Update MultiQC module
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‎conf/modules/bwa_index.config‎

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process {
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withName: BWA_INDEX {
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publishDir = [
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[
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path: { "${params.outdir}/${params.aligner}/reference_genome" },
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mode: params.publish_dir_mode,
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pattern: "*",
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enabled: params.save_reference
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]
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]
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}
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}

‎conf/modules/picard_addorreplacereadgroups.config‎

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process {
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withName: PICARD_ADDORREPLACEREADGROUPS {
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ext.args = "--RGID 1 --RGLB lib1 --RGPL illumina --RGPU unit1 --RGSM sample1"
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// Don't publish intermediate BAMs - these are only used as input to PICARD_MARKDUPLICATES
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publishDir = [
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enabled: false
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]
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}
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}

‎conf/modules/samtools_idxstats.config‎

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process {
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withName: SAMTOOLS_IDXSTATS {
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publishDir = [
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[
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path: { "${params.outdir}/${params.aligner}/alignments/samtools_stats/" },
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mode: params.publish_dir_mode,
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pattern: "*.idxstats"
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]
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]
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}
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}

‎conf/modules/samtools_index.config‎

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@@ -6,13 +6,13 @@ process {
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path: { "${params.outdir}/${params.aligner}/deduplicated/" },
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mode: params.publish_dir_mode,
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pattern: "*.bai",
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enabled: !params.skip_deduplication
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enabled: !(params.skip_deduplication || params.rrbs)
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],
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[
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path: { "${params.outdir}/${params.aligner}/alignments/" },
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mode: params.publish_dir_mode,
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pattern: "*.bai",
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enabled: params.skip_deduplication
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enabled: params.skip_deduplication || params.rrbs
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]
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]
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}

‎conf/modules/samtools_sort.config‎

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path: { "${params.outdir}/${params.aligner}/alignments/" },
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mode: params.publish_dir_mode,
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pattern: "*.sorted.bam",
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enabled: params.skip_deduplication || params.save_align_intermeds
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enabled: params.skip_deduplication || params.rrbs || params.save_align_intermeds
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]
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]
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}

‎conf/subworkflows/fasta_index_methylseq.config‎

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@@ -2,3 +2,4 @@ includeConfig "../modules/gunzip.config"
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includeConfig "../modules/bismark_genomepreparation.config"
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includeConfig "../modules/samtools_faidx.config"
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includeConfig "../modules/bwameth_index.config"
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includeConfig "../modules/bwa_index.config"

‎conf/subworkflows/fastq_align_dedup_bismark.config‎

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@@ -10,20 +10,22 @@ includeConfig "../modules/bismark_summary.config"
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// Override SAMTOOLS_SORT for bismark workflow
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// In bismark, deduplication (BISMARK_DEDUPLICATE) happens BEFORE sorting,
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// so the BAM input to SAMTOOLS_SORT is already deduplicated when skip_deduplication is false
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// Note: RRBS also skips deduplication, so we check for both params.skip_deduplication and params.rrbs
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process {
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withName: SAMTOOLS_SORT {
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ext.prefix = params.skip_deduplication ? { "${meta.id}.sorted" } : { "${meta.id}.deduplicated.sorted" }
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withName: 'NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:SAMTOOLS_SORT' {
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ext.prefix = { (params.skip_deduplication || params.rrbs) ? "${meta.id}.sorted" : "${meta.id}.deduplicated.sorted" }
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publishDir = [
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[
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path: { "${params.outdir}/${params.aligner}/deduplicated/" },
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mode: params.publish_dir_mode,
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pattern: "*.deduplicated.sorted.bam"
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pattern: "*.deduplicated.sorted.bam",
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enabled: !(params.skip_deduplication || params.rrbs)
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],
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[
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path: { "${params.outdir}/${params.aligner}/alignments/" },
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mode: params.publish_dir_mode,
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pattern: "*.sorted.bam",
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enabled: params.skip_deduplication
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enabled: params.skip_deduplication || params.rrbs
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]
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]
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}

‎conf/subworkflows/fastq_align_dedup_bwamem.config‎

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includeConfig "../modules/bwamem_align.config"
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includeConfig "../modules/picard_addorreplacereadgroups.config"
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includeConfig "../modules/picard_markduplicates.config"
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includeConfig "../modules/samtools_index.config"
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includeConfig "../modules/samtools_stats.config"
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includeConfig "../modules/samtools_flagstat.config"
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includeConfig "../modules/samtools_idxstats.config"
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// Note: SAMTOOLS_INDEX is called twice in this workflow with different requirements:
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// 1. BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX - indexes alignment BAMs (before dedup)
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// 2. FASTQ_ALIGN_DEDUP_BWAMEM:SAMTOOLS_INDEX - indexes deduplicated BAMs (after markdup)
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// We need full process paths to distinguish them.
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process {
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// SAMTOOLS_SORT in BAM_SORT_STATS_SAMTOOLS - publish to alignments when skip_deduplication
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withName: 'NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BWAMEM:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
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ext.prefix = { "${meta.id}.sorted" }
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publishDir = [
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[
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path: { "${params.outdir}/${params.aligner}/alignments/" },
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mode: params.publish_dir_mode,
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pattern: "*.sorted.bam",
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enabled: params.skip_deduplication
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]
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]
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}
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// SAMTOOLS_INDEX in BAM_SORT_STATS_SAMTOOLS - only publish when skip_deduplication
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withName: 'NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BWAMEM:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
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publishDir = [
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[
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path: { "${params.outdir}/${params.aligner}/alignments/" },
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mode: params.publish_dir_mode,
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pattern: "*.bai",
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enabled: params.skip_deduplication
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]
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]
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}
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// SAMTOOLS_INDEX after PICARD_MARKDUPLICATES - publish to deduplicated when deduplication runs
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withName: 'NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BWAMEM:SAMTOOLS_INDEX' {
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publishDir = [
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[
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path: { "${params.outdir}/${params.aligner}/deduplicated/" },
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mode: params.publish_dir_mode,
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pattern: "*.bai",
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enabled: !params.skip_deduplication
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]
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]
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}
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}

‎conf/subworkflows/fastq_align_dedup_bwameth.config‎

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path: { "${params.outdir}/${params.aligner}/alignments/" },
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mode: params.publish_dir_mode,
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pattern: "*.bam.bai",
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enabled: params.save_align_intermeds
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enabled: params.save_align_intermeds || params.skip_deduplication || params.rrbs
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]
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]
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}
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[
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path: { "${params.outdir}/${params.aligner}/deduplicated/" },
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mode: params.publish_dir_mode,
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pattern: "*.bam.bai"
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pattern: "*.bam.bai",
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enabled: !(params.skip_deduplication || params.rrbs)
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]
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]
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}

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