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 <max.u.garcia@gmail.com>

---------

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

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"