From 021f5f0a2200c4ea9d5275f3c6fc8ceaf3a74675 Mon Sep 17 00:00:00 2001 From: sofstam Date: Fri, 31 Mar 2023 10:28:36 +0200 Subject: [PATCH] Remove samtools/bam2fq module --- modules.json | 175 ++++++++++++++++------- modules/nf-core/samtools/bam2fq/main.nf | 56 -------- modules/nf-core/samtools/bam2fq/meta.yml | 55 ------- 3 files changed, 127 insertions(+), 159 deletions(-) delete mode 100644 modules/nf-core/samtools/bam2fq/main.nf delete mode 100644 modules/nf-core/samtools/bam2fq/meta.yml diff --git a/modules.json b/modules.json index 65d8b70..63de285 100644 --- a/modules.json +++ b/modules.json @@ -8,222 +8,301 @@ "adapterremoval": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bbmap/bbduk": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bowtie2/align": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bowtie2/build": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bracken/bracken": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bracken/combinebrackenoutputs": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/fastq": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "centrifuge/centrifuge": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "centrifuge/kreport": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "diamond/blastx": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "falco": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/falco/falco.diff" }, "fastp": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastqc": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "filtlong": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gunzip": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "kaiju/kaiju": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "kaiju/kaiju2krona": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "kaiju/kaiju2table": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "kraken2/kraken2": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "krakentools/combinekreports": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "krakentools/kreport2krona": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "krakenuniq/preloadedkrakenuniq": { "branch": "master", "git_sha": "a6eb17f65b3ee5761c25c075a6166c9f76733cee", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "krona/ktimporttaxonomy": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "krona/ktimporttext": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "malt/run": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "megan/rma2info": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "metaphlan3/mergemetaphlantables": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "metaphlan3/metaphlan3": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "minimap2/align": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "minimap2/index": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "motus/merge": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "motus/profile": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "porechop/porechop": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff" }, "prinseqplusplus": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] - }, - "samtools/bam2fq": { - "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/fastq": { "branch": "master", "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/index": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/stats": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/view": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "taxpasta/merge": { "branch": "master", "git_sha": "ffa9641ee18f88aff974257cb50ba3cf8f7d143c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf deleted file mode 100644 index 0b06352..0000000 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ /dev/null @@ -1,56 +0,0 @@ -process SAMTOOLS_BAM2FQ { - tag "$meta.id" - label 'process_low' - - conda "bioconda::samtools=1.16.1" - container "${ 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(inputbam) - val split - - output: - tuple val(meta), path("*.fq.gz"), emit: reads - 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}" - - if (split){ - """ - samtools \\ - bam2fq \\ - $args \\ - -@ $task.cpus \\ - -1 ${prefix}_1.fq.gz \\ - -2 ${prefix}_2.fq.gz \\ - -0 ${prefix}_other.fq.gz \\ - -s ${prefix}_singleton.fq.gz \\ - $inputbam - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS - """ - } else { - """ - samtools \\ - bam2fq \\ - $args \\ - -@ $task.cpus \\ - $inputbam | gzip --no-name > ${prefix}_interleaved.fq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS - """ - } -} diff --git a/modules/nf-core/samtools/bam2fq/meta.yml b/modules/nf-core/samtools/bam2fq/meta.yml deleted file mode 100644 index 319a60c..0000000 --- a/modules/nf-core/samtools/bam2fq/meta.yml +++ /dev/null @@ -1,55 +0,0 @@ -name: samtools_bam2fq -description: | - The module uses bam2fq method from samtools to - convert a SAM, BAM or CRAM file to FASTQ format -keywords: - - bam2fq - - samtools - - fastq -tools: - - samtools: - description: Tools for dealing with SAM, BAM and CRAM files - homepage: None - documentation: http://www.htslib.org/doc/1.1/samtools.html - tool_dev_url: None - doi: "" - licence: ["MIT"] - -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - inputbam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - split: - type: boolean - description: | - TRUE/FALSE value to indicate if reads should be separated into - /1, /2 and if present other, or singleton. - Note: choosing TRUE will generate 4 different files. - Choosing FALSE will produce a single file, which will be interleaved in case - the input contains paired reads. - -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" - - reads: - type: file - description: | - FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton) - or a single interleaved .fq.gz file if the user chooses not to split the reads. - pattern: "*.fq.gz" - -authors: - - "@lescai"