Added ability to auto-create samplesheet for nf-core/phageannotator

.github/workflows/ci.yml

@@ -62,6 +62,7 @@ jobs:
             test_adapterremoval,
             test_binrefinement,
             test_virus_identification,
+            test_samplesheet,
           ]
     steps:
       - name: Free some space

conf/modules.config

@@ -741,6 +741,21 @@ process {
         ]
     }
 
+    withName: MAG_TO_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            enabled: false
+        ]
+    }
+
+    withName: 'MAG_MERGE_SAMPLESHEET' {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },

conf/test_samplesheet.config

@@ -0,0 +1,47 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/mag -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    input                         = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.multirun.csv'
+    centrifuge_db                 = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_cf.tar.gz"
+    kraken2_db                    = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_kraken.tgz"
+    skip_krona                    = true
+    min_length_unbinned_contigs   = 1
+    max_unbinned_contigs          = 2
+    busco_db                      = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
+    busco_clean                   = true
+    skip_gtdbtk                   = true
+    skip_concoct                  = true
+
+    // For computational efficiency
+    nf_core_pipeline            = 'phageannotator'
+    coassemble_group            = false
+    skip_binning                = true
+    skip_prokka                 = true
+    skip_spadeshybrid           = true
+    skip_quast                  = true
+    skip_prodigal               = true
+    skip_krona                  = true
+    skip_adapter_trimming       = true
+    skip_metabat2               = true
+    skip_maxbin2                = true
+    skip_busco                  = true
+}

modules.json

@@ -36,6 +36,11 @@
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
+                    "cat/cat": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
                     "cat/fastq": {
                         "branch": "master",
                         "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",

modules/local/mag_merge_samplesheet.nf

@@ -0,0 +1,27 @@
+process MAG_MERGE_SAMPLESHEET {
+
+    conda "conda-forge::sed=4.7"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'nf-core/ubuntu:20.04' }"
+
+    input:
+    path ('samplesheets/*')
+
+    output:
+    path "samplesheet.csv", emit: samplesheet
+    path "versions.yml"   , emit: versions
+
+    script:
+    """
+    head -n 1 `ls ./samplesheets/* | head -n 1` > samplesheet.csv
+    for fileid in `ls ./samplesheets/*`; do
+        awk 'NR>1' \$fileid >> samplesheet.csv
+    done
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/local/mag_to_samplesheet.nf

@@ -0,0 +1,40 @@
+process MAG_TO_SAMPLESHEET {
+    tag "$meta.id"
+
+    executor 'local'
+    memory 100.MB
+
+    input:
+    val meta
+    val pipeline
+
+    output:
+    tuple val(meta), path("*samplesheet.csv"), emit: samplesheet
+
+    exec:
+    //
+    // Create samplesheet containing metadata
+    //
+
+    // Add nf-core pipeline specific entries
+    if (pipeline) {
+        if (pipeline == 'phageannotator') {
+            pipeline_map = [
+                sample  : "${meta.id}",
+                group   : "${meta.group}",
+                fastq_1 : meta.fastq_1,
+                fastq_2 : meta.fastq_2,
+                fasta   : meta.fasta
+            ]
+        }
+    }
+
+    // Create a samplesheet
+    samplesheet  = pipeline_map.keySet().collect{ '"' + it + '"'}.join(",") + '\n'
+    samplesheet += pipeline_map.values().collect{ '"' + it + '"'}.join(",")
+
+    // Write samplesheet to file
+    def samplesheet_file = task.workDir.resolve("${meta.id}.samplesheet.csv")
+    samplesheet_file.text = samplesheet
+
+}