Umitools prepareforrsem (nf-core#4897)

* Add umitools/prepareforrsem

* Remove trailing newlines

* Fix software env

* appease eclint

* fix linting

* fix comment

* Don't snapshot python version

* Readd snapshot file

* Apply suggestions from code review

Co-authored-by: Maxime U Garcia <[email protected]>

---------

Co-authored-by: Maxime U Garcia <[email protected]>

modules/nf-core/umitools/prepareforrsem/environment.yml

@@ -0,0 +1,7 @@
+name: umitools_prepareforrsem
+channels:
+ - conda-forge
+ - bioconda
+ - defaults
+dependencies:
+ - bioconda::umi_tools=1.1.4

modules/nf-core/umitools/prepareforrsem/main.nf

@@ -0,0 +1,34 @@
+process UMITOOLS_PREPAREFORRSEM {
+ tag "$meta.id"
+ label 'process_medium'
+
+ conda "${moduleDir}/environment.yml"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.4--py38hbff2b2d_1' :
+ 'biocontainers/umi_tools:1.1.4--py38hbff2b2d_1' }"
+
+ input:
+ tuple val(meta), path(bam), path(bai)
+
+ output:
+ tuple val(meta), path('*.bam'), emit: bam
+ tuple val(meta), path('*.log'), emit: log
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ template 'prepare-for-rsem.py'
+
+ stub:
+ """
+ touch ${meta.id}.bam
+ touch ${meta.id}.log
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
+ END_VERSIONS
+ """
+}

modules/nf-core/umitools/prepareforrsem/meta.yml

@@ -0,0 +1,53 @@
+name: umitools_prepareforrsem
+description: Make the output from umi_tools dedup or group compatible with RSEM
+keywords:
+ - umitools
+ - rsem
+ - salmon
+ - dedup
+tools:
+ - umi_tools:
+ description: >
+ UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
+ documentation: https://umi-tools.readthedocs.io/en/latest/
+ license: ["MIT"]
+input:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - bam:
+ type: file
+ description: |
+ BAM file containing reads to be deduplicated via UMIs.
+ pattern: "*.{bam}"
+ - bai:
+ type: file
+ description: |
+ BAM index files corresponding to the input BAM file.
+ pattern: "*.{bai}"
+output:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - bam:
+ type: file
+ description: Prepared BAM file.
+ pattern: "*.{bam}"
+ - log:
+ type: file
+ description: File with logging information
+ pattern: "*.{log}"
+ - versions:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+authors:
+ - "@drpatelh"
+ - "@pinin4fjords"
+maintainers:
+ - "@drpatelh"
+ - "@pinin4fjords"