diff --git a/modules.json b/modules.json
index 4a090fd6e6f1a31b03ba0a8e2fbe9ea1f2633747..d7443e6bb4a6189effd0c714a08fcbc4dcd6c291 100644
--- a/modules.json
+++ b/modules.json
@@ -2,24 +2,83 @@
"name": "nf-core/hic",
"homePage": "https://github.com/nf-core/hic",
"repos": {
- "nf-core/modules": {
- "bowtie2/align": {
- "git_sha": "61f68913fefc20241ceccb671b104230b2d775d7"
+ "https://github.com/nf-core/modules.git": {
+ "modules": {
+ "nf-core": {
+ "bowtie2/align": {
+ "branch": "master",
+ "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "installed_by": [
+ "modules"
+ ]
+ },
+ "bowtie2/build": {
+ "branch": "master",
+ "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "installed_by": [
+ "modules"
+ ]
+ },
+ "cooler/balance": {
+ "branch": "master",
+ "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "installed_by": [
+ "modules"
+ ]
+ },
+ "cooler/cload": {
+ "branch": "master",
+ "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "installed_by": [
+ "modules"
+ ]
+ },
+ "cooler/dump": {
+ "branch": "master",
+ "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "installed_by": [
+ "modules"
+ ]
+ },
+ "cooler/makebins": {
+ "branch": "master",
+ "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "installed_by": [
+ "modules"
+ ]
+ },
+ "cooler/zoomify": {
+ "branch": "master",
+ "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "installed_by": [
+ "modules"
+ ]
+ },
+ "custom/dumpsoftwareversions": {
+ "branch": "master",
+ "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "installed_by": [
+ "modules"
+ ]
+ },
+ "custom/getchromsizes": {
+ "branch": "master",
+ "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "installed_by": [
+ "modules"
+ ]
+ },
+ "fastqc": {
+ "branch": "master",
+ "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "installed_by": [
+ "modules"
+ ]
+ }
+ }
},
- "bowtie2/build": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "cooler/zoomify": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "custom/dumpsoftwareversions": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "custom/getchromsizes": {
- "git_sha": "213403187932dbbdd936a04474cc8cd8abae7a08"
- },
- "fastqc": {
- "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
+ "subworkflows": {
+ "nf-core": {}
}
}
}
diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf
new file mode 100644
index 0000000000000000000000000000000000000000..3d851866a30b4f629881864516f0789f6cae9443
--- /dev/null
+++ b/modules/nf-core/bowtie2/align/main.nf
@@ -0,0 +1,71 @@
+process BOWTIE2_ALIGN {
+ tag "$meta.id"
+ label "process_high"
+
+ conda "bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' :
+ 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }"
+
+ input:
+ tuple val(meta) , path(reads)
+ tuple val(meta2), path(index)
+ val save_unaligned
+ val sort_bam
+
+ output:
+ tuple val(meta), path("*.bam") , emit: bam
+ tuple val(meta), path("*.log") , emit: log
+ tuple val(meta), path("*fastq.gz"), emit: fastq, optional:true
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def args = task.ext.args ?: ""
+ def args2 = task.ext.args2 ?: ""
+ def prefix = task.ext.prefix ?: "${meta.id}"
+
+ def unaligned = ""
+ def reads_args = ""
+ if (meta.single_end) {
+ unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ""
+ reads_args = "-U ${reads}"
+ } else {
+ unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ""
+ reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
+ }
+
+ def samtools_command = sort_bam ? 'sort' : 'view'
+
+ """
+ INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\\.rev.1.bt2\$//"`
+ [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/\\.rev.1.bt2l\$//"`
+ [ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
+
+ bowtie2 \\
+ -x \$INDEX \\
+ $reads_args \\
+ --threads $task.cpus \\
+ $unaligned \\
+ $args \\
+ 2> ${prefix}.bowtie2.log \\
+ | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
+
+ if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
+ mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
+ fi
+
+ if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
+ mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
+ fi
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+ END_VERSIONS
+ """
+}
diff --git a/modules/nf-core/modules/bowtie2/align/meta.yml b/modules/nf-core/bowtie2/align/meta.yml
similarity index 74%
rename from modules/nf-core/modules/bowtie2/align/meta.yml
rename to modules/nf-core/bowtie2/align/meta.yml
index f80421eca42c51c7238770d44466f9de978e01ae..c8e9a001290d0feddaa121424a5a9c65ae568396 100644
--- a/modules/nf-core/modules/bowtie2/align/meta.yml
+++ b/modules/nf-core/bowtie2/align/meta.yml
@@ -2,7 +2,9 @@ name: bowtie2_align
description: Align reads to a reference genome using bowtie2
keywords:
- align
+ - map
- fasta
+ - fastq
- genome
- reference
tools:
@@ -25,10 +27,24 @@ input:
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
+ - meta2:
+ type: map
+ description: |
+ Groovy Map containing reference information
+ e.g. [ id:'test', single_end:false ]
- index:
type: file
description: Bowtie2 genome index files
pattern: "*.ebwt"
+ - save_unaligned:
+ type: boolean
+ description: |
+ Save reads that do not map to the reference (true) or discard them (false)
+ (default: false)
+ - sort_bam:
+ type: boolean
+ description: use samtools sort (true) or samtools view (false)
+ pattern: "true or false"
output:
- bam:
type: file
diff --git a/modules/nf-core/modules/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
similarity index 80%
rename from modules/nf-core/modules/bowtie2/build/main.nf
rename to modules/nf-core/bowtie2/build/main.nf
index a4da62d073b5353cfdd6bff727cc12a86692706b..551893af3b3bb1a3955f1cc7c0b50735c6fded8d 100644
--- a/modules/nf-core/modules/bowtie2/build/main.nf
+++ b/modules/nf-core/bowtie2/build/main.nf
@@ -2,17 +2,17 @@ process BOWTIE2_BUILD {
tag "$fasta"
label 'process_high'
- conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
+ conda "bioconda::bowtie2=2.4.4"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' :
'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
input:
- path fasta
+ tuple val(meta), path(fasta)
output:
- path 'bowtie2' , emit: index
- path "versions.yml" , emit: versions
+ tuple val(meta), path('bowtie2') , emit: index
+ path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/modules/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml
similarity index 74%
rename from modules/nf-core/modules/bowtie2/build/meta.yml
rename to modules/nf-core/bowtie2/build/meta.yml
index 2da9a217163fae0e1b392af5ce6473c62e074c25..0240224d532af842d762c5c947fff6e84e5be113 100644
--- a/modules/nf-core/modules/bowtie2/build/meta.yml
+++ b/modules/nf-core/bowtie2/build/meta.yml
@@ -16,10 +16,20 @@ tools:
doi: 10.1038/nmeth.1923
licence: ["GPL-3.0-or-later"]
input:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing reference information
+ e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: Input genome fasta file
output:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing reference information
+ e.g. [ id:'test', single_end:false ]
- index:
type: file
description: Bowtie2 genome index files
diff --git a/modules/nf-core/cooler/balance/main.nf b/modules/nf-core/cooler/balance/main.nf
new file mode 100644
index 0000000000000000000000000000000000000000..4173a3c1291df7e25e3529d9ab8f2b6f8d1240b7
--- /dev/null
+++ b/modules/nf-core/cooler/balance/main.nf
@@ -0,0 +1,39 @@
+process COOLER_BALANCE {
+ tag "$meta.id"
+ label 'process_high'
+
+ conda "bioconda::cooler=0.8.11"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0':
+ 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+
+ input:
+ tuple val(meta), path(cool), val(resolution)
+
+ output:
+ tuple val(meta), path("${prefix}.${extension}"), emit: cool
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def args = task.ext.args ?: ''
+ prefix = task.ext.prefix ?: "${meta.id}"
+ suffix = resolution ? "::/resolutions/$resolution" : ""
+ extension = cool.getExtension()
+ if ("$cool" == "${prefix}.${extension}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+ """
+ cp ${cool} ${prefix}.${extension}
+
+ cooler balance \\
+ $args \\
+ -p ${task.cpus} \\
+ ${prefix}.${extension}${suffix}
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
+ END_VERSIONS
+ """
+}
diff --git a/modules/nf-core/cooler/balance/meta.yml b/modules/nf-core/cooler/balance/meta.yml
new file mode 100644
index 0000000000000000000000000000000000000000..af1a780002701ad6bbf7d64105e5e8153098f5ec
--- /dev/null
+++ b/modules/nf-core/cooler/balance/meta.yml
@@ -0,0 +1,45 @@
+name: "cooler_balance"
+description: Run matrix balancing on a cool file
+keywords:
+ - balance
+tools:
+ - "cooler":
+ description: Sparse binary format for genomic interaction matrices
+ homepage: https://open2c.github.io/cooler/
+ documentation: https://cooler.readthedocs.io/en/latest/index.html
+ tool_dev_url: https://github.com/open2c/cooler
+ doi: "10.1093/bioinformatics/btz540"
+ licence: ["BSD-3-Clause"]
+
+input:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - cool:
+ type: file
+ description: Path to COOL file
+ pattern: "*.{cool,mcool}"
+ - resolution:
+ type: value
+ description: Resolution
+
+output:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - versions:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+ - cool:
+ type: file
+ description: Output COOL file balancing weigths
+ pattern: "*.cool"
+
+authors:
+ - "@nservant"
+ - "@muffato"
diff --git a/modules/nf-core/cooler/cload/main.nf b/modules/nf-core/cooler/cload/main.nf
new file mode 100644
index 0000000000000000000000000000000000000000..80d61f07336f81233a6bd8ffb116e5a25e57048d
--- /dev/null
+++ b/modules/nf-core/cooler/cload/main.nf
@@ -0,0 +1,39 @@
+process COOLER_CLOAD {
+ tag "$meta.id"
+ label 'process_high'
+
+ conda "bioconda::cooler=0.8.11"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
+ 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+
+ input:
+ tuple val(meta), path(pairs), path(index), val(cool_bin)
+ path chromsizes
+
+ output:
+ tuple val(meta), path("*.cool"), val(cool_bin), emit: cool
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ def nproc = args.contains('pairix') || args.contains('tabix')? "--nproc $task.cpus" : ''
+
+ """
+ cooler cload \\
+ $args \\
+ $nproc \\
+ ${chromsizes}:${cool_bin} \\
+ $pairs \\
+ ${prefix}.cool
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
+ END_VERSIONS
+ """
+}
diff --git a/modules/nf-core/cooler/cload/meta.yml b/modules/nf-core/cooler/cload/meta.yml
new file mode 100644
index 0000000000000000000000000000000000000000..8513aaec1ed8558f850367f453ee55eb9d378b11
--- /dev/null
+++ b/modules/nf-core/cooler/cload/meta.yml
@@ -0,0 +1,53 @@
+name: cooler_cload
+description: Create a cooler from genomic pairs and bins
+keywords:
+ - cool
+tools:
+ - cooler:
+ description: Sparse binary format for genomic interaction matrices
+ homepage: https://open2c.github.io/cooler/
+ documentation: https://cooler.readthedocs.io/en/latest/index.html
+ tool_dev_url: https://github.com/open2c/cooler
+ doi: "10.1093/bioinformatics/btz540"
+ licence: ["BSD-3-clause"]
+
+input:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - pairs:
+ type: file
+ description: Path to contacts (i.e. read pairs) file.
+ - index:
+ type: file
+ description: Path to index file of the contacts.
+ - cool_bin:
+ type: value
+ description: Bins size in bp
+ - chromsizes:
+ type: file
+ description: Path to a chromsizes file.
+
+output:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - version:
+ type: file
+ description: File containing software version
+ pattern: "versions.yml"
+ - cool:
+ type: file
+ description: Output COOL file path
+ pattern: "*.cool"
+ - cool_bin:
+ type: value
+ description: Bins size in bp
+
+authors:
+ - "@jianhong"
+ - "@muffato"
diff --git a/modules/nf-core/cooler/dump/main.nf b/modules/nf-core/cooler/dump/main.nf
new file mode 100644
index 0000000000000000000000000000000000000000..b46c78cf35ec6b40276e2d792635f97b9909ab55
--- /dev/null
+++ b/modules/nf-core/cooler/dump/main.nf
@@ -0,0 +1,35 @@
+process COOLER_DUMP {
+ tag "$meta.id"
+ label 'process_high'
+
+ conda "bioconda::cooler=0.8.11"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
+ 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+
+ input:
+ tuple val(meta), path(cool), val(resolution)
+
+ output:
+ tuple val(meta), path("*.bedpe"), emit: bedpe
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ def suffix = resolution ? "::/resolutions/$resolution" : ""
+ """
+ cooler dump \\
+ $args \\
+ -o ${prefix}.bedpe \\
+ $cool$suffix
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
+ END_VERSIONS
+ """
+}
diff --git a/modules/nf-core/cooler/dump/meta.yml b/modules/nf-core/cooler/dump/meta.yml
new file mode 100644
index 0000000000000000000000000000000000000000..fe60523eb3556a6bb2187be0563c3fd6f2cbf5cf
--- /dev/null
+++ b/modules/nf-core/cooler/dump/meta.yml
@@ -0,0 +1,45 @@
+name: cooler_dump
+description: Dump a cooler’s data to a text stream.
+keywords:
+ - dump
+tools:
+ - cooler:
+ description: Sparse binary format for genomic interaction matrices
+ homepage: https://open2c.github.io/cooler/
+ documentation: https://cooler.readthedocs.io/en/latest/index.html
+ tool_dev_url: https://github.com/open2c/cooler
+ doi: "10.1093/bioinformatics/btz540"
+ licence: ["BSD-3-Clause"]
+
+input:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - cool:
+ type: file
+ description: Path to COOL file
+ pattern: "*.{cool,mcool}"
+ - resolution:
+ type: value
+ description: Resolution
+
+output:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - versions:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+ - bedpe:
+ type: file
+ description: Output text file
+ pattern: "*.bedpe"
+
+authors:
+ - "@jianhong"
+ - "@muffato"
diff --git a/modules/nf-core/cooler/makebins/main.nf b/modules/nf-core/cooler/makebins/main.nf
new file mode 100644
index 0000000000000000000000000000000000000000..7f0826197e99e9e79107359a8c65d7d60346dc49
--- /dev/null
+++ b/modules/nf-core/cooler/makebins/main.nf
@@ -0,0 +1,34 @@
+process COOLER_MAKEBINS {
+ tag "${meta.id}}"
+ label 'process_low'
+
+ conda "bioconda::cooler=0.8.11"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0':
+ 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+
+ input:
+ tuple val(meta), path(chromsizes), val(cool_bin)
+
+ output:
+ tuple val(meta), path("*.bed"), emit: bed
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ """
+ cooler makebins \\
+ $args \\
+ ${chromsizes} \\
+ ${cool_bin} > ${prefix}.bed
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
+ END_VERSIONS
+ """
+}
diff --git a/modules/nf-core/cooler/makebins/meta.yml b/modules/nf-core/cooler/makebins/meta.yml
new file mode 100644
index 0000000000000000000000000000000000000000..33fd8eb63f4a3225d3d03eb028578b2c1eeeaa5d
--- /dev/null
+++ b/modules/nf-core/cooler/makebins/meta.yml
@@ -0,0 +1,34 @@
+name: "cooler_makebins"
+description: Generate fixed-width genomic bins
+keywords:
+ - makebins
+tools:
+ - "cooler":
+ description: Sparse binary format for genomic interaction matrices
+ homepage: https://open2c.github.io/cooler/
+ documentation: https://cooler.readthedocs.io/en/latest/index.html
+ tool_dev_url: https://github.com/open2c/cooler
+ doi: "10.1093/bioinformatics/btz540"
+ licence: ["BSD-3-Clause"]
+
+input:
+ - chromsize:
+ type: file
+ description: Path to chromosome size file
+ - cool_bin:
+ type: value
+ description: Resolution (bin size) in base pairs
+
+output:
+ - versions:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+ - bed:
+ type: file
+ description: Genome segmentation at a fixed resolution as a BED file.
+ pattern: "*.bed"
+
+authors:
+ - "@nservant"
+ - "@muffato"
diff --git a/modules/nf-core/modules/cooler/zoomify/main.nf b/modules/nf-core/cooler/zoomify/main.nf
similarity index 93%
rename from modules/nf-core/modules/cooler/zoomify/main.nf
rename to modules/nf-core/cooler/zoomify/main.nf
index 942282c0d6a8ab161502a375863185579bae9f47..f1cd8df79d02b8630c31de0620521cef0cdd6df0 100644
--- a/modules/nf-core/modules/cooler/zoomify/main.nf
+++ b/modules/nf-core/cooler/zoomify/main.nf
@@ -2,7 +2,7 @@ process COOLER_ZOOMIFY {
tag "$meta.id"
label 'process_high'
- conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
+ conda "bioconda::cooler=0.8.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
diff --git a/modules/nf-core/modules/cooler/zoomify/meta.yml b/modules/nf-core/cooler/zoomify/meta.yml
similarity index 93%
rename from modules/nf-core/modules/cooler/zoomify/meta.yml
rename to modules/nf-core/cooler/zoomify/meta.yml
index d9e12b0587d3500e9592402bd5788615cad9d17a..57f554861b25d4ca9edac66c73ff306a4d9f9390 100644
--- a/modules/nf-core/modules/cooler/zoomify/meta.yml
+++ b/modules/nf-core/cooler/zoomify/meta.yml
@@ -5,7 +5,7 @@ keywords:
tools:
- cooler:
description: Sparse binary format for genomic interaction matrices
- homepage: https://cooler.readthedocs.io/en/latest/index.html
+ homepage: https://open2c.github.io/cooler/
documentation: https://cooler.readthedocs.io/en/latest/index.html
tool_dev_url: https://github.com/open2c/cooler
doi: "10.1093/bioinformatics/btz540"
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
similarity index 79%
rename from modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
rename to modules/nf-core/custom/dumpsoftwareversions/main.nf
index 327d5100560d84eb0020b60acf0db2922497991b..3df21765b90921413962c3bb5ca44d117d829297 100644
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -1,11 +1,11 @@
process CUSTOM_DUMPSOFTWAREVERSIONS {
- label 'process_low'
+ label 'process_single'
// Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
- conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
+ conda "bioconda::multiqc=1.13"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
- 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
+ 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
+ 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
input:
path versions
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
similarity index 100%
rename from modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
rename to modules/nf-core/custom/dumpsoftwareversions/meta.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
new file mode 100755
index 0000000000000000000000000000000000000000..da03340857c4c90957c79c9f892030bc1bb397a3
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+
+
+"""Provide functions to merge multiple versions.yml files."""
+
+
+import yaml
+import platform
+from textwrap import dedent
+
+
+def _make_versions_html(versions):
+ """Generate a tabular HTML output of all versions for MultiQC."""
+ html = [
+ dedent(
+ """\\
+ <style>
+ #nf-core-versions tbody:nth-child(even) {
+ background-color: #f2f2f2;
+ }
+ </style>
+ <table class="table" style="width:100%" id="nf-core-versions">
+ <thead>
+ <tr>
+ <th> Process Name </th>
+ <th> Software </th>
+ <th> Version </th>
+ </tr>
+ </thead>
+ """
+ )
+ ]
+ for process, tmp_versions in sorted(versions.items()):
+ html.append("<tbody>")
+ for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
+ html.append(
+ dedent(
+ f"""\\
+ <tr>
+ <td><samp>{process if (i == 0) else ''}</samp></td>
+ <td><samp>{tool}</samp></td>
+ <td><samp>{version}</samp></td>
+ </tr>
+ """
+ )
+ )
+ html.append("</tbody>")
+ html.append("</table>")
+ return "\\n".join(html)
+
+
+def main():
+ """Load all version files and generate merged output."""
+ versions_this_module = {}
+ versions_this_module["${task.process}"] = {
+ "python": platform.python_version(),
+ "yaml": yaml.__version__,
+ }
+
+ with open("$versions") as f:
+ versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
+
+ # aggregate versions by the module name (derived from fully-qualified process name)
+ versions_by_module = {}
+ for process, process_versions in versions_by_process.items():
+ module = process.split(":")[-1]
+ try:
+ if versions_by_module[module] != process_versions:
+ raise AssertionError(
+ "We assume that software versions are the same between all modules. "
+ "If you see this error-message it means you discovered an edge-case "
+ "and should open an issue in nf-core/tools. "
+ )
+ except KeyError:
+ versions_by_module[module] = process_versions
+
+ versions_by_module["Workflow"] = {
+ "Nextflow": "$workflow.nextflow.version",
+ "$workflow.manifest.name": "$workflow.manifest.version",
+ }
+
+ versions_mqc = {
+ "id": "software_versions",
+ "section_name": "${workflow.manifest.name} Software Versions",
+ "section_href": "https://github.com/${workflow.manifest.name}",
+ "plot_type": "html",
+ "description": "are collected at run time from the software output.",
+ "data": _make_versions_html(versions_by_module),
+ }
+
+ with open("software_versions.yml", "w") as f:
+ yaml.dump(versions_by_module, f, default_flow_style=False)
+ with open("software_versions_mqc.yml", "w") as f:
+ yaml.dump(versions_mqc, f, default_flow_style=False)
+
+ with open("versions.yml", "w") as f:
+ yaml.dump(versions_this_module, f, default_flow_style=False)
+
+
+if __name__ == "__main__":
+ main()
diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf
new file mode 100644
index 0000000000000000000000000000000000000000..580f87feade7280bb8d520551aa61f0021b3b88d
--- /dev/null
+++ b/modules/nf-core/custom/getchromsizes/main.nf
@@ -0,0 +1,44 @@
+process CUSTOM_GETCHROMSIZES {
+ tag "$fasta"
+ label 'process_single'
+
+ conda "bioconda::samtools=1.16.1"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
+ 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
+
+ input:
+ tuple val(meta), path(fasta)
+
+ output:
+ tuple val(meta), path ("*.sizes"), emit: sizes
+ tuple val(meta), path ("*.fai") , emit: fai
+ tuple val(meta), path ("*.gzi") , emit: gzi, optional: true
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def args = task.ext.args ?: ''
+ """
+ samtools faidx $fasta
+ cut -f 1,2 ${fasta}.fai > ${fasta}.sizes
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ getchromsizes: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ END_VERSIONS
+ """
+
+ stub:
+ """
+ touch ${fasta}.fai
+ touch ${fasta}.sizes
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ getchromsizes: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ END_VERSIONS
+ """
+}
diff --git a/modules/nf-core/modules/custom/getchromsizes/meta.yml b/modules/nf-core/custom/getchromsizes/meta.yml
similarity index 62%
rename from modules/nf-core/modules/custom/getchromsizes/meta.yml
rename to modules/nf-core/custom/getchromsizes/meta.yml
index ee6c257185a41746801ae1cccaaef1d31379ddd7..219ca1d8e07166c23e28089ae5067b5937cc6f8d 100644
--- a/modules/nf-core/modules/custom/getchromsizes/meta.yml
+++ b/modules/nf-core/custom/getchromsizes/meta.yml
@@ -14,12 +14,22 @@ tools:
licence: ["MIT"]
input:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: FASTA file
- pattern: "*.{fasta}"
+ pattern: "*.{fa,fasta,fna,fas}"
output:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
- sizes:
type: file
description: File containing chromosome lengths
@@ -28,11 +38,16 @@ output:
type: file
description: FASTA index file
pattern: "*.{fai}"
+ - gzi:
+ type: file
+ description: Optional gzip index file for compressed inputs
+ pattern: "*.gzi"
- versions:
type: file
- description: File containing software version
+ description: File containing software versions
pattern: "versions.yml"
authors:
- "@tamara-hodgetts"
- "@chris-cheshire"
+ - "@muffato"
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
new file mode 100644
index 0000000000000000000000000000000000000000..9ae5838158b28d2ae49270133fbbfe0ea673e991
--- /dev/null
+++ b/modules/nf-core/fastqc/main.nf
@@ -0,0 +1,51 @@
+process FASTQC {
+ tag "$meta.id"
+ label 'process_medium'
+
+ conda "bioconda::fastqc=0.11.9"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
+ 'quay.io/biocontainers/fastqc:0.11.9--0' }"
+
+ input:
+ tuple val(meta), path(reads)
+
+ output:
+ tuple val(meta), path("*.html"), emit: html
+ tuple val(meta), path("*.zip") , emit: zip
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ // Make list of old name and new name pairs to use for renaming in the bash while loop
+ def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
+ def rename_to = old_new_pairs*.join(' ').join(' ')
+ def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+ """
+ printf "%s %s\\n" $rename_to | while read old_name new_name; do
+ [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
+ done
+ fastqc $args --threads $task.cpus $renamed_files
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+ END_VERSIONS
+ """
+
+ stub:
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ """
+ touch ${prefix}.html
+ touch ${prefix}.zip
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+ END_VERSIONS
+ """
+}
diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
similarity index 100%
rename from modules/nf-core/modules/fastqc/meta.yml
rename to modules/nf-core/fastqc/meta.yml
diff --git a/modules/nf-core/modules/bowtie2/align/main.nf b/modules/nf-core/modules/bowtie2/align/main.nf
deleted file mode 100644
index c233f955d10b8812541b80725939b4d1768e0d32..0000000000000000000000000000000000000000
--- a/modules/nf-core/modules/bowtie2/align/main.nf
+++ /dev/null
@@ -1,81 +0,0 @@
-process BOWTIE2_ALIGN {
- tag "$meta.id"
- label 'process_high'
-
- conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6' : null)
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' :
- 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' }"
-
- input:
- tuple val(meta), path(reads)
- path index
- val save_unaligned
-
- output:
- tuple val(meta), path('*.bam') , emit: bam
- tuple val(meta), path('*.log') , emit: log
- tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
- path "versions.yml" , emit: versions
-
- when:
- task.ext.when == null || task.ext.when
-
- script:
- def args = task.ext.args ?: ''
- def args2 = task.ext.args2 ?: ''
- def prefix = task.ext.prefix ?: "${meta.id}"
- if (meta.single_end) {
- def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
- """
- INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
- [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
- [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
- bowtie2 \\
- -x \$INDEX \\
- -U $reads \\
- --threads $task.cpus \\
- $unaligned \\
- $args \\
- 2> ${prefix}.bowtie2.log \\
- | samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
- samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
- pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
- END_VERSIONS
- """
- } else {
- def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
- """
- INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
- [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
- [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
- bowtie2 \\
- -x \$INDEX \\
- -1 ${reads[0]} \\
- -2 ${reads[1]} \\
- --threads $task.cpus \\
- $unaligned \\
- $args \\
- 2> ${prefix}.bowtie2.log \\
- | samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
-
- if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
- mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
- fi
- if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
- mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
- fi
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
- samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
- pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
- END_VERSIONS
- """
- }
-}
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
deleted file mode 100644
index d13903925467e97e353f0a4e6bcf9f6cdb8a3664..0000000000000000000000000000000000000000
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ /dev/null
@@ -1,89 +0,0 @@
-#!/usr/bin/env python
-
-import yaml
-import platform
-from textwrap import dedent
-
-
-def _make_versions_html(versions):
- html = [
- dedent(
- """\\
- <style>
- #nf-core-versions tbody:nth-child(even) {
- background-color: #f2f2f2;
- }
- </style>
- <table class="table" style="width:100%" id="nf-core-versions">
- <thead>
- <tr>
- <th> Process Name </th>
- <th> Software </th>
- <th> Version </th>
- </tr>
- </thead>
- """
- )
- ]
- for process, tmp_versions in sorted(versions.items()):
- html.append("<tbody>")
- for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
- html.append(
- dedent(
- f"""\\
- <tr>
- <td><samp>{process if (i == 0) else ''}</samp></td>
- <td><samp>{tool}</samp></td>
- <td><samp>{version}</samp></td>
- </tr>
- """
- )
- )
- html.append("</tbody>")
- html.append("</table>")
- return "\\n".join(html)
-
-
-versions_this_module = {}
-versions_this_module["${task.process}"] = {
- "python": platform.python_version(),
- "yaml": yaml.__version__,
-}
-
-with open("$versions") as f:
- versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
-
-# aggregate versions by the module name (derived from fully-qualified process name)
-versions_by_module = {}
-for process, process_versions in versions_by_process.items():
- module = process.split(":")[-1]
- try:
- assert versions_by_module[module] == process_versions, (
- "We assume that software versions are the same between all modules. "
- "If you see this error-message it means you discovered an edge-case "
- "and should open an issue in nf-core/tools. "
- )
- except KeyError:
- versions_by_module[module] = process_versions
-
-versions_by_module["Workflow"] = {
- "Nextflow": "$workflow.nextflow.version",
- "$workflow.manifest.name": "$workflow.manifest.version",
-}
-
-versions_mqc = {
- "id": "software_versions",
- "section_name": "${workflow.manifest.name} Software Versions",
- "section_href": "https://github.com/${workflow.manifest.name}",
- "plot_type": "html",
- "description": "are collected at run time from the software output.",
- "data": _make_versions_html(versions_by_module),
-}
-
-with open("software_versions.yml", "w") as f:
- yaml.dump(versions_by_module, f, default_flow_style=False)
-with open("software_versions_mqc.yml", "w") as f:
- yaml.dump(versions_mqc, f, default_flow_style=False)
-
-with open("versions.yml", "w") as f:
- yaml.dump(versions_this_module, f, default_flow_style=False)
diff --git a/modules/nf-core/modules/custom/getchromsizes/main.nf b/modules/nf-core/modules/custom/getchromsizes/main.nf
deleted file mode 100644
index 0eabf3a4c3cdd9a862154859e1241990052dc2d4..0000000000000000000000000000000000000000
--- a/modules/nf-core/modules/custom/getchromsizes/main.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-process CUSTOM_GETCHROMSIZES {
- tag "$fasta"
- label 'process_low'
-
- conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
- 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
-
- input:
- path fasta
-
- output:
- path '*.sizes' , emit: sizes
- path '*.fai' , emit: fai
- path "versions.yml", emit: versions
-
- when:
- task.ext.when == null || task.ext.when
-
- script:
- def args = task.ext.args ?: ''
- """
- samtools faidx $fasta
- cut -f 1,2 ${fasta}.fai > ${fasta}.sizes
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- custom: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
- END_VERSIONS
- """
-}
diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/modules/fastqc/main.nf
deleted file mode 100644
index 05730368b2d43e0eaac6b13a69f07ed54d1ed2cb..0000000000000000000000000000000000000000
--- a/modules/nf-core/modules/fastqc/main.nf
+++ /dev/null
@@ -1,59 +0,0 @@
-process FASTQC {
- tag "$meta.id"
- label 'process_medium'
-
- conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
- 'quay.io/biocontainers/fastqc:0.11.9--0' }"
-
- input:
- tuple val(meta), path(reads)
-
- output:
- tuple val(meta), path("*.html"), emit: html
- tuple val(meta), path("*.zip") , emit: zip
- path "versions.yml" , emit: versions
-
- when:
- task.ext.when == null || task.ext.when
-
- script:
- def args = task.ext.args ?: ''
- // Add soft-links to original FastQs for consistent naming in pipeline
- def prefix = task.ext.prefix ?: "${meta.id}"
- if (meta.single_end) {
- """
- [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
- fastqc $args --threads $task.cpus ${prefix}.fastq.gz
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
- END_VERSIONS
- """
- } else {
- """
- [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
- [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
- fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
- END_VERSIONS
- """
- }
-
- stub:
- def prefix = task.ext.prefix ?: "${meta.id}"
- """
- touch ${prefix}.html
- touch ${prefix}.zip
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
- END_VERSIONS
- """
-}