Stage input in folder

nf-core · Nov 20, 2024 · 8e9cde6 · 8e9cde6
1 parent a488422
commit 8e9cde6
Show file tree

Hide file tree

Showing 4 changed files with 43 additions and 260 deletions.
diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -8,26 +8,23 @@ process BCFTOOLS_PLUGINSPLIT {
         'biocontainers/bcftools:1.20--h8b25389_0' }"
 
     input:
-    tuple val(meta), path(vcf), path(tbi)
+    tuple val(meta), path(vcf, stageAs: "?/*"), path(tbi, stageAs: "?/*")
     path(samples)
     path(groups)
     path(regions)
     path(targets)
 
     output:
-    tuple val(meta), path("outputDir/*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
-    tuple val(meta), path("outputDir/*.tbi")                    , emit: tbi, optional: true
-    tuple val(meta), path("outputDir/*.csi")                    , emit: csi, optional: true
-    path "versions.yml"                                 , emit: versions
+    tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
+    tuple val(meta), path("*.tbi")                    , emit: tbi, optional: true
+    tuple val(meta), path("*.csi")                    , emit: csi, optional: true
+    path "versions.yml"                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    // Here the default prefix is an empty string as the filename is created by the plugin
-    // and the prefix is instead added to the output files in the script
-    def prefix = task.ext.prefix ?: ""
 
     def samples_arg = samples ? "--samples-file ${samples}" : ""
     def groups_arg  = groups  ? "--groups-file ${groups}"   : ""
@@ -42,13 +39,7 @@ process BCFTOOLS_PLUGINSPLIT {
         ${groups_arg} \\
         ${regions_arg} \\
         ${targets_arg} \\
-        --output outputDir
-
-    if [ -n "${prefix}" ]; then
-        for file in outputDir/*; do
-            mv \$file outputDir/${prefix}\${file##*/}
-        done
-    fi
+        --output .
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -58,7 +49,6 @@ process BCFTOOLS_PLUGINSPLIT {
 
     stub:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: ""
 
     def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
                 args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
@@ -72,23 +62,15 @@ process BCFTOOLS_PLUGINSPLIT {
     def determination_file = samples ?: targets
     def create_cmd = extension.matches("vcf|bcf") ? "touch " : "echo '' | gzip > "
     """
-    mkdir -p outputDir
-
     cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt
     while IFS= read -r filename;
-        do ${create_cmd} "outputDir/\$filename";
+        do ${create_cmd} "./\$filename";
         if [ -n "${index}" ]; then
             index_file=\$(sed -e 's/\$/.${index}/' <<< \$filename);
-            touch outputDir/\$index_file;
+            touch ./\$index_file;
         fi;
     done < files.txt
 
-    if [ -n "${prefix}" ]; then
-        for file in outputDir/*; do
-            mv \$file outputDir/${prefix}\${file##*/}
-        done
-    fi
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')

diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
@@ -67,7 +67,6 @@ nextflow_process {
     }
 
     test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi") {
-
         config "./nextflow.config"
 
         when {
@@ -99,38 +98,8 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - [ vcf, tbi ], [], [], [], [], - tbi with prefix") {
-
-        config "./nextflow_prefix.config"
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz.tbi', checkIfExists: true)
-                ]
-                input[1] = []
-                input[2] = []
-                input[3] = []
-                input[4] = []
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
     test("homo_sapiens - [ vcf, tbi ], [], [], [], [], - error no sample") {
-
-        config "./nextflow_prefix.config"
+        config "./nextflow.config"
 
         when {
             process {
@@ -151,7 +120,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.failed },
-                { assert process.errorReport.contains("No samples to split: dbsnp_146.hg38.vcf.gz") }
+                { assert process.errorReport.contains("No samples to split: 1/dbsnp_146.hg38.vcf.gz") }
             )
         }
 
@@ -244,36 +213,4 @@ nextflow_process {
         }
 
     }
-
-    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with prefix -stub") {
-
-        tag "test"
-        config "./nextflow_prefix.config"
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
-                ]
-                input[1] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
-                    .collectFile(name:"samples.txt", newLine:true)
-                input[2] = []
-                input[3] = []
-                input[4] = []
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
 }