Adding plasflow module

modules/nf-core/samtools/cramsize/main.nf

@@ -0,0 +1,35 @@
+process SAMTOOLS_CRAMSIZE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::samtools=1.17"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0':
+        'biocontainers/samtools:1.17--h00cdaf9_0' }"
+
+    input:
+    tuple val(meta), path(cram)
+
+    output:
+    tuple val(meta), path("*.size"), emit: size
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    samtools \\
+        cram-size \\
+        $args \\
+        -o ${cram.baseName}.size \\
+        $cram
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        : \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+}

modules/nf-core/samtools/cramsize/meta.yml

@@ -0,0 +1,42 @@
+name: samtools_cramsize
+description: List CRAM Content-ID and Data-Series sizes
+keywords:
+  - cram-size
+  - cram
+  - size
+tools:
+  - samtools:
+      description: |
+        SAMtools is a set of utilities for interacting with and post-processing
+        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+        These files are generated as output by short read aligners like BWA.
+      homepage: http://www.htslib.org/
+      documentation: http://www.htslib.org/doc/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - cram:
+      type: file
+      description: CRAM file
+      pattern: "*.cram"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - size:
+      type: file
+      description: Size information file
+      pattern: "*.size"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@limrp"

tests/config/pytest_modules.yml

@@ -3047,6 +3047,10 @@ samtools/coverage:
   - modules/nf-core/samtools/coverage/**
   - tests/modules/nf-core/samtools/coverage/**
 
+samtools/cramsize:
+  - modules/nf-core/samtools/cramsize/**
+  - tests/modules/nf-core/samtools/cramsize/**
+
 samtools/depth:
   - modules/nf-core/samtools/depth/**
   - tests/modules/nf-core/samtools/depth/**

tests/modules/nf-core/samtools/cramsize/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_CRAMSIZE } from '../../../../../modules/nf-core/samtools/cramsize/main.nf'
+
+workflow test_samtools_cramsize {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    SAMTOOLS_CRAMSIZE ( input )
+}

tests/modules/nf-core/samtools/cramsize/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

tests/modules/nf-core/samtools/cramsize/test.yml

@@ -0,0 +1,13 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml /cramsize
+- name: "samtools cramsize"
+  command: nextflow run ./tests/modules/nf-core/samtools/cramsize -entry test_samtools_cramsize -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/cramsize/nextflow.config
+  tags:
+    - "samtools"
+    - "samtools/cramsize"
+  files:
+    - path: "output/samtools/test.bam"
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: "output/samtools/versions.yml"
+      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
+