Merge pull request #339 from JoseEspinosa/fixes

Some fixes
nf-core · Apr 18, 2023 · 3b94a84 · 3b94a84
2 parents 8f4d262 + aece0fb
commit 3b94a84
Show file tree

Hide file tree

Showing 40 changed files with 1,304 additions and 460 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Updated pipeline template to [nf-core/tools 2.7.2](https://github.com/nf-core/tools/releases/tag/2.7.2)
 - [[#317](https://github.com/nf-core/chipseq/issues/317)] Added metro map
 - [[#288](https://github.com/nf-core/chipseq/issues/291)] Bump `chromap` version 2 and enable all the steps below chromap again when paired-end data is processed.
+- [[#311](https://github.com/nf-core/chipseq/issues/311)] Add back `--skip_spp` parameter which was unintentionally removed from the code.
+- Install available nf-core subworkflows and refactor code accordingly
+- [[#318](https://github.com/nf-core/chipseq/issues/318)] Update `bowtie2/align` module to fix issue when downloading its singularity image.
 
 ## [[2.0.0](https://github.com/nf-core/chipseq/releases/tag/2.0.0)] - 2022-10-03
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -122,7 +122,7 @@ process {
 
 if (!(params.skip_fastqc || params.skip_qc)) {
     process {
-        withName: '.*:FASTQC_TRIMGALORE:FASTQC' {
+        withName: 'FASTQC' {
             ext.args = '--quiet'
             publishDir = [
                 [
@@ -142,11 +142,17 @@ if (!(params.skip_fastqc || params.skip_qc)) {
 
 if (!params.skip_trimming) {
     process {
-        withName: '.*:FASTQC_TRIMGALORE:TRIMGALORE' {
-            ext.args   = [
-                '--fastqc',
-                params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : ''
-            ].join(' ').trim()
+        withName: 'TRIMGALORE' {
+            ext.args   = {
+                [
+                    '--fastqc',
+                    params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : '',
+                    params.clip_r1 > 0 ? "--clip_r1 ${params.clip_r1}" : '',
+                    params.clip_r2 > 0 ? "--clip_r2 ${params.clip_r2}" : '',
+                    params.three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${params.three_prime_clip_r1}" : '',
+                    params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : ''
+                ].join(' ').trim()
+            }
             publishDir = [
                 [
                     path: { "${params.outdir}/trimgalore/fastqc" },
@@ -175,7 +181,7 @@ if (!params.skip_trimming) {
 }
 
 process {
-    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_.*:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' {
+    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
         ext.prefix = { "${meta.id}.Lb.sorted" }
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/library" },
@@ -185,7 +191,7 @@ process {
         ]
     }
 
-    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_.*:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' {
+    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/library" },
             mode: params.publish_dir_mode,
@@ -194,7 +200,7 @@ process {
         ]
     }
 
-    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_.*' {
+    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_.*' {
         ext.prefix = { "${meta.id}.Lb.sorted.bam" }
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/library/samtools_stats/" },
@@ -208,11 +214,13 @@ process {
 if (params.aligner == 'bwa') {
     process {
         withName: 'BWA_MEM' {
-            ext.args   = { [
-                            '-M',
-                            params.bwa_min_score ? " -T ${params.bwa_min_score}" : '',
-                            meta.read_group ? "-R ${meta.read_group}": ''
-                        ].join(' ').trim() }
+            ext.args   = {
+                [
+                    '-M',
+                    params.bwa_min_score ? " -T ${params.bwa_min_score}" : '',
+                    meta.read_group ? "-R ${meta.read_group}": ''
+                ].join(' ').trim()
+            }
             ext.args2  = '-bhS -F 0x0100 -O BAM'
             ext.prefix = { "${meta.id}.Lb" }
             publishDir = [
@@ -351,8 +359,15 @@ process {
     }
 
     // Should only be published when paired end data is used and save_align_intermeds is true
-    withName: 'BAM_FILTER' {
-        ext.prefix = { meta.single_end ?  "${meta.id}.mLb.noPublish" : "${meta.id}.mLb.flT.sorted" }
+    withName: 'BAMTOOLS_FILTER' {
+        ext.args   = {
+                [
+                    meta.single_end ? '-F 0x004' : '-F 0x004 -F 0x0008 -f 0x001',
+                    params.keep_dups ? '' : '-F 0x0400',
+                    params.keep_multi_map ? '' : '-q 1'
+                ].join(' ').trim()
+        }
+        ext.prefix = { meta.single_end ?  "${meta.id}.mLb.noPublish" : "${meta.id}.mLb.flT.sorted" } //TODO check with atacseq
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/mergedLibrary" },
             mode: params.publish_dir_mode,
@@ -367,7 +382,7 @@ process {
         publishDir = [ enabled: false ]
     }
 
-    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' {
+    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:BAM_FILTER_BAMTOOLS:SAMTOOLS_SORT' {
         ext.prefix = { "${meta.id}.mLb.clN.sorted" }
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/mergedLibrary" },
@@ -376,7 +391,7 @@ process {
         ]
     }
 
-    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' {
+    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:BAM_FILTER_BAMTOOLS:SAMTOOLS_INDEX' {
         ext.prefix = { "${meta.id}.mLb.clN.sorted" }
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/mergedLibrary" },
@@ -385,7 +400,7 @@ process {
         ]
     }
 
-    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
+    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:BAM_FILTER_BAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
         ext.prefix = { "${meta.id}.mLb.clN.sorted.bam" }
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/mergedLibrary/samtools_stats" },

diff --git a/modules.json b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "bowtie2/align": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": ["modules"]
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": ["fastq_align_bowtie2", "modules"]
                     },
                     "bowtie2/build": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "bwa/index": {
@@ -23,12 +23,12 @@
                     "bwa/mem": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_align_bwa", "modules"]
                     },
                     "chromap/chromap": {
                         "branch": "master",
-                        "git_sha": "d6b7b1f108dab88b0269a4331767c36a1a8da960",
-                        "installed_by": ["modules"]
+                        "git_sha": "b7f0dbc07af00c0ccdc7c2df06efee8786e976ac",
+                        "installed_by": ["fastq_align_chromap", "modules"]
                     },
                     "chromap/index": {
                         "branch": "master",
@@ -42,9 +42,8 @@
                     },
                     "custom/getchromsizes": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/custom/getchromsizes/custom-getchromsizes.diff"
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": ["modules"]
                     },
                     "deeptools/computematrix": {
                         "branch": "master",
@@ -69,7 +68,7 @@
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules", "fastq_fastqc_umitools_trimgalore"]
                     },
                     "gffread": {
                         "branch": "master",
@@ -108,7 +107,7 @@
                     },
                     "picard/collectmultiplemetrics": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "75027bf77472b1f4fd2cdd7e46f83119dfb0f2c6",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {
@@ -129,27 +128,27 @@
                     "samtools/flagstat": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": ["modules"]
+                        "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": ["modules"]
+                        "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": ["modules"]
+                        "installed_by": ["bam_sort_stats_samtools", "modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": ["modules"]
+                        "installed_by": ["bam_sort_stats_samtools", "modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": ["modules"]
+                        "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "subread/featurecounts": {
                         "branch": "master",
@@ -159,19 +158,58 @@
                     "trimgalore": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules", "fastq_fastqc_umitools_trimgalore"]
                     },
                     "ucsc/bedgraphtobigwig": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
                         "installed_by": ["modules"]
                     },
+                    "umitools/extract": {
+                        "branch": "master",
+                        "git_sha": "ffe2f5865f608848e440a52b73c304ea79aaf818",
+                        "installed_by": ["fastq_fastqc_umitools_trimgalore"]
+                    },
                     "untar": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
                         "installed_by": ["modules"]
                     }
                 }
+            },
+            "subworkflows": {
+                "nf-core": {
+                    "bam_sort_stats_samtools": {
+                        "branch": "master",
+                        "git_sha": "3911652a6b24249358f79e8b8466338d63efb2a2",
+                        "installed_by": ["fastq_align_bowtie2", "fastq_align_chromap", "fastq_align_bwa"]
+                    },
+                    "bam_stats_samtools": {
+                        "branch": "master",
+                        "git_sha": "b4b7f89e7fd6d2293f0c176213f710e0bcdaf19e",
+                        "installed_by": ["bam_sort_stats_samtools"]
+                    },
+                    "fastq_align_bowtie2": {
+                        "branch": "master",
+                        "git_sha": "ac75f79157ecc64283a2b3a559f1ba90bc0f2259",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "fastq_align_bwa": {
+                        "branch": "master",
+                        "git_sha": "901fab507683647b43e7032f3ae9e4c234eb68eb",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "fastq_align_chromap": {
+                        "branch": "master",
+                        "git_sha": "ac75f79157ecc64283a2b3a559f1ba90bc0f2259",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "fastq_fastqc_umitools_trimgalore": {
+                        "branch": "master",
+                        "git_sha": "100caf3506850ffcc04953f724a97f422940c377",
+                        "installed_by": ["subworkflows"]
+                    }
+                }
             }
         }
     }

diff --git a/modules/local/bam_filter.nf → modules/local/bamtools_filter.nf b/modules/local/bam_filter.nf → modules/local/bamtools_filter.nf
@@ -1,7 +1,4 @@
-/*
- * Filter BAM file
- */
-process BAM_FILTER {
+process BAMTOOLS_FILTER {
     tag "$meta.id"
     label 'process_medium'
 
@@ -20,19 +17,18 @@ process BAM_FILTER {
     tuple val(meta), path("*.bam"), emit: bam
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
-    def prefix           = task.ext.prefix ?: "${meta.id}"
-    def filter_params    = meta.single_end ? '-F 0x004' : '-F 0x004 -F 0x0008 -f 0x001'
-    def dup_params       = params.keep_dups ? '' : '-F 0x0400'
-    def multimap_params  = params.keep_multi_map ? '' : '-q 1'
-    def blacklist_params = params.blacklist ? "-L $bed" : ''
-    def config           = meta.single_end ? bamtools_filter_se_config : bamtools_filter_pe_config
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def blacklist = bed ? "-L $bed" : ''
+    def config = meta.single_end ? bamtools_filter_se_config : bamtools_filter_pe_config
     """
     samtools view \\
-        $filter_params \\
-        $dup_params \\
-        $multimap_params \\
-        $blacklist_params \\
+        $args \\
+        $blacklist \\
         -b $bam \\
         | bamtools filter \\
             -out ${prefix}.bam \\

diff --git a/modules/local/star_align.nf b/modules/local/star_align.nf
@@ -11,6 +11,7 @@ process STAR_ALIGN {
     input:
     tuple val(meta), path(reads)
     path  index
+    val seq_center
 
     output:
     tuple val(meta), path('*d.out.bam')       , emit: bam
@@ -25,10 +26,13 @@ process STAR_ALIGN {
     tuple val(meta), path('*fastq.gz')               , optional:true, emit: fastq
     tuple val(meta), path('*.tab')                   , optional:true, emit: tab
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def seq_center = params.seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$params.seq_center' 'SM:$prefix'" : "--outSAMattrRGline ID:$prefix 'SM:$prefix'"
+    def seq_center_tag = seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$seq_center' 'SM:$prefix'" : "--outSAMattrRGline ID:$prefix 'SM:$prefix'"
     def out_sam_type = (args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted'
     def mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : ''
     """
@@ -38,7 +42,7 @@ process STAR_ALIGN {
         --runThreadN $task.cpus \\
         --outFileNamePrefix $prefix. \\
         $out_sam_type \\
-        $seq_center \\
+        $seq_center_tag \\
         $args
     $mv_unsorted_bam
     if [ -f ${prefix}.Unmapped.out.mate1 ]; then

diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf