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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| /* | ||
| * Pairtools - merge | ||
| * Merge multiple sorted pairs files | ||
| */ | ||
|
|
||
| process PAIRTOOLS_MERGE { | ||
| tag "${meta.id}" | ||
| label 'process_medium' | ||
|
|
||
|
|
||
| // Pinning numpy to 1.23 until https://github.com/open2c/pairtools/issues/170 is resolved | ||
| // Not an issue with the biocontainers because they were built prior to numpy 1.24 | ||
| conda "bioconda::pairtools=1.0.2 conda-forge::numpy=1.23" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/pairtools:1.0.2--py39h2a9f597_0' : | ||
| 'biocontainers/pairtools:1.0.2--py39h2a9f597_0' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(allpairs) | ||
|
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||
| output: | ||
| tuple val(meta), path("*pairs.gz"), emit:pairs | ||
| path("versions.yml"), emit:versions | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}_merged" | ||
| """ | ||
| pairtools merge \ | ||
| ${args} \ | ||
| --nproc ${task.cpus} \ | ||
| -o ${prefix}.pairs.gz \ | ||
| ${allpairs} | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools, version //') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| /* | ||
| * Pairtools - Split | ||
| * Split a .pairsam file into .pairs and .sam | ||
| */ | ||
|
|
||
| process PAIRTOOLS_SPLIT { | ||
| tag "${meta.id}" | ||
| label 'process_medium' | ||
|
|
||
| // Pinning numpy to 1.23 until https://github.com/open2c/pairtools/issues/170 is resolved | ||
| // Not an issue with the biocontainers because they were built prior to numpy 1.24 | ||
| conda "bioconda::pairtools=1.0.2 conda-forge::numpy=1.23" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/pairtools:1.0.2--py39h2a9f597_0' : | ||
| 'biocontainers/pairtools:1.0.2--py39h2a9f597_0' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(pairs) | ||
|
|
||
| output: | ||
| tuple val(meta), path("*.split.pairs.gz"), emit:pairs | ||
| tuple val(meta), path("*.bam"), optional:true, emit:bam | ||
| tuple val(meta), path("*.txt"), optional: true, emit:stats | ||
| path("versions.yml"), emit:versions | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| pairtools split \ | ||
| --nproc-in ${task.cpus} --nproc-out ${task.cpus} \ | ||
| --output-pairs ${prefix}.split.pairs.gz \ | ||
| ${args} \ | ||
| ${pairs} | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools, version //') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| /* | ||
| * Pairtools - Stats | ||
| * Statistics on pairs file | ||
| */ | ||
|
|
||
| process PAIRTOOLS_STATS { | ||
| tag "${meta.id}" | ||
| label 'process_low' | ||
|
|
||
| // Pinning numpy to 1.23 until https://github.com/open2c/pairtools/issues/170 is resolved | ||
| // Not an issue with the biocontainers because they were built prior to numpy 1.24 | ||
| conda "bioconda::pairtools=1.0.2 conda-forge::numpy=1.23" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/pairtools:1.0.2--py39h2a9f597_0' : | ||
| 'biocontainers/pairtools:1.0.2--py39h2a9f597_0' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(pairs) | ||
|
|
||
| output: | ||
| tuple val(meta), path("*txt"), emit:stats | ||
| path("versions.yml"), emit:versions | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}_stats" | ||
| """ | ||
| pairtools stats \ | ||
| ${args} \ | ||
| --nproc-in ${task.cpus} --nproc-out ${task.cpus} \ | ||
| -o ${prefix}.txt \ | ||
| ${pairs} | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools, version //') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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