refactor: split out pixelator dependency in CHECK_SAMPLESHEET

bin/check_samplesheet.py

@@ -8,13 +8,12 @@
 import argparse
 import csv
 import logging
+import re
 import sys
 import urllib.parse
-from collections import Counter
+from os import PathLike
 from pathlib import Path, PurePath
-import re
 from typing import Iterable, List, MutableMapping, Optional, Set
-from os import PathLike
 
 logger = logging.getLogger()
 

conf/modules.config

@@ -19,12 +19,6 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: 'SAMPLESHEET_CHECK' {
-        if (params.pixelator_container) {
-            container = params.pixelator_container
-        }
-    }
-
     withName: COLLECT_METADATA {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },

modules/local/pixelator/list_designs.nf

@@ -0,0 +1,26 @@
+process PIXELATOR_LIST_DESIGNS {
+    label 'process_single'
+
+    // TODO: Update once pixelator is public in bioconda
+    conda "local::pixelator=0.12.0"
+    container "ghcr.io/pixelgentechnologies/pixelator:0.12.0"
+
+    output:
+    path "design_options.txt"     , emit: designs
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    pixelator single-cell --list-designs $args > design_options.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pixelator: \$(echo \$(pixelator --version 2>/dev/null) | sed 's/pixelator, version //g' )
+    END_VERSIONS
+    """
+}

modules/local/samplesheet_check.nf

@@ -2,12 +2,14 @@ process SAMPLESHEET_CHECK {
     tag "$samplesheet"
     label 'process_single'
 
-    // TODO: Update once pixelator is public in bioconda
-    conda "local::pixelator=0.12.0"
-    container "ghcr.io/pixelgentechnologies/pixelator:0.12.0"
+    conda "conda-forge::python=3.8.3"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
+        'biocontainers/python:3.8.3' }"
 
     input:
     path samplesheet
+    path design_options
     val samplesheet_path
 
     output:
@@ -21,19 +23,16 @@ process SAMPLESHEET_CHECK {
     def args = task.ext.args ?: ''
 
     """
-    pixelator single-cell --list-designs > design_options.txt
-
     check_samplesheet.py \\
         $samplesheet \\
         samplesheet.valid.csv \\
         --samplesheet-path $samplesheet_path \\
-        --design-options design_options.txt \\
+        --design-options $design_options \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python --version | sed 's/Python //g')
-        pixelator: \$(echo \$(pixelator --version 2>/dev/null) | sed 's/pixelator, version //g' )
     END_VERSIONS
     """
 }

subworkflows/local/input_check.nf

@@ -2,15 +2,24 @@
 // Check input samplesheet and get read channels
 //
 
-include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'
+include { SAMPLESHEET_CHECK }        from '../../modules/local/samplesheet_check'
+include { PIXELATOR_LIST_DESIGNS }   from '../../modules/local/pixelator/list_designs.nf'
 
 workflow INPUT_CHECK {
     take:
     samplesheet                                // file: /path/to/samplesheet.csv
 
     main:
-    ch_samplesheet_rows = SAMPLESHEET_CHECK ( samplesheet, samplesheet.toUri() )
-        .csv
+
+    PIXELATOR_LIST_DESIGNS()
+
+    SAMPLESHEET_CHECK (
+        samplesheet,
+        PIXELATOR_LIST_DESIGNS.out.designs,
+        samplesheet.toUri()
+    )
+
+    ch_samplesheet_rows = SAMPLESHEET_CHECK.out.csv
         .splitCsv ( header:true, sep:',' )
 
     reads = ch_samplesheet_rows.map { create_fastq_channel(it) }