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Some fixes #339

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merged 24 commits into from
Apr 18, 2023
Merged

Some fixes #339

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b4ad530
Add back skip_spp parameter
JoseEspinosa Apr 17, 2023
77907aa
Install fastq_fastqc_umitools_trimgalore subworkflow
JoseEspinosa Apr 17, 2023
d67a0fd
Install fastq_align_bwa subworkflow
JoseEspinosa Apr 17, 2023
8b93ec2
Install fastq_align_bowtie2 subworkflow
JoseEspinosa Apr 17, 2023
356ccd2
Install fastq_align_chromap subworkflow
JoseEspinosa Apr 17, 2023
c8739ed
use the FASTQ_FASTQC_UMITOOLS_TRIMGALORE subworkflow insead of fastq…
JoseEspinosa Apr 17, 2023
8af9cb2
Use FASTQ_ALIGN_BWA subworkflow
JoseEspinosa Apr 17, 2023
d7f074a
Use FASTQ_ALIGN_BOWTIE2 subworkflow
JoseEspinosa Apr 18, 2023
28de291
Install custom/getchromsizes and picard/collectmultiplemetrics
JoseEspinosa Apr 18, 2023
4c462b3
Remove substituted modules and subworkflows
JoseEspinosa Apr 18, 2023
3a33ed9
Rename bamtools/filter
JoseEspinosa Apr 18, 2023
0f70b6d
add align_star local subworkflow
JoseEspinosa Apr 18, 2023
ccbc71c
Refactor and rename bam_filter_bamtools
JoseEspinosa Apr 18, 2023
0230090
Refactor code to use nf-core official subworkflows
JoseEspinosa Apr 18, 2023
3165a73
Simplify code
JoseEspinosa Apr 18, 2023
30312c3
changelog
JoseEspinosa Apr 18, 2023
603db63
Resolved arguments for bamtools_filteer
JoseEspinosa Apr 18, 2023
2637d88
Update bowtie2/align to fix the container download
JoseEspinosa Apr 18, 2023
6a75945
Remove code used for view
JoseEspinosa Apr 18, 2023
b00897d
Feed missing arguments to star subworkflow
JoseEspinosa Apr 18, 2023
be423bf
Update chromap/chromap
JoseEspinosa Apr 18, 2023
7cc3041
Update star_align
JoseEspinosa Apr 18, 2023
403a8e5
Update changelog
JoseEspinosa Apr 18, 2023
aece0fb
Update bowtie2/build
JoseEspinosa Apr 18, 2023
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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

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53 changes: 34 additions & 19 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,7 @@ process {

if (!(params.skip_fastqc || params.skip_qc)) {
process {
withName: '.*:FASTQC_TRIMGALORE:FASTQC' {
withName: 'FASTQC' {
ext.args = '--quiet'
publishDir = [
[
Expand All @@ -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" },
Expand Down Expand Up @@ -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" },
Expand All @@ -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,
Expand All @@ -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/" },
Expand All @@ -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 = [
Expand Down Expand Up @@ -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,
Expand All @@ -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" },
Expand All @@ -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" },
Expand All @@ -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" },
Expand Down
72 changes: 55 additions & 17 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand All @@ -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",
Expand All @@ -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",
Expand All @@ -69,7 +68,7 @@
"fastqc": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": ["modules", "fastq_fastqc_umitools_trimgalore"]
},
"gffread": {
"branch": "master",
Expand Down Expand Up @@ -108,7 +107,7 @@
},
"picard/collectmultiplemetrics": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "75027bf77472b1f4fd2cdd7e46f83119dfb0f2c6",
"installed_by": ["modules"]
},
"picard/markduplicates": {
Expand All @@ -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",
Expand All @@ -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"]
}
}
}
}
}
Expand Down
24 changes: 10 additions & 14 deletions modules/local/bam_filter.nf → modules/local/bamtools_filter.nf
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Original file line number Diff line number Diff line change
@@ -1,7 +1,4 @@
/*
* Filter BAM file
*/
process BAM_FILTER {
process BAMTOOLS_FILTER {
tag "$meta.id"
label 'process_medium'

Expand All @@ -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 \\
Expand Down
8 changes: 6 additions & 2 deletions modules/local/star_align.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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" : ''
"""
Expand All @@ -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
Expand Down
16 changes: 8 additions & 8 deletions modules/nf-core/bowtie2/align/main.nf
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