remove params.outdir from modules and subworfklows tests (#5007)

* remove params.outdir from modules and subworfklows tests * update usage of params outdir * update more tests * Apply suggestions from code review * Apply suggestions from code review * update snap * update snap * update even more snaps * remove obsolete snaps
nf-core · Feb 28, 2024 · 5caf764 · 5caf764
1 parent dcfa9a1
commit 5caf764
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Showing 21 changed files with 205 additions and 87 deletions.
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
@@ -15,7 +15,6 @@ nextflow_process {
             params {
                 settings_path = '/tmp/.ncbi'
                 settings_file  = "${params.settings_path}/user-settings.mkfg"
-                outdir         = "$outputDir"
             }
 
             process {

diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config
@@ -4,8 +4,6 @@ params.settings_file = "${params.settings_path}/user-settings.mkfg"
 env.NCBI_SETTINGS = params.settings_file
 
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     withName: CUSTOM_SRATOOLSNCBISETTINGS {
         containerOptions = {
             (workflow.containerEngine == 'singularity') ?

diff --git a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap
diff --git a/modules/nf-core/mtmalign/align/tests/main.nf.test.snap b/modules/nf-core/mtmalign/align/tests/main.nf.test.snap
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -23,10 +23,6 @@ nextflow_process {
         }
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_single_end', single_end:true ], files]}
@@ -58,10 +54,6 @@ nextflow_process {
         }
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_paired_end', single_end:false ], files]}

diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -10,9 +10,6 @@ nextflow_process {
     test("sratools/prefetch") {
 
         when {
-            params {
-                outdir = "output"
-            }
             process {
                 """
                 input[0] = Channel.of([ [ id:'test', single_end:false ], 'DRR000774' ])
@@ -33,9 +30,6 @@ nextflow_process {
     test("sratools/prefetch with sralite") {
 
         when {
-            params {
-                outdir = "output"
-            }
             process {
                 """
                 input[0] = Channel.of([ [ id:'test', single_end:false ], 'SRR1170046' ])

diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
diff --git a/modules/nf-core/tcoffee/align/tests/main.nf.test.snap b/modules/nf-core/tcoffee/align/tests/main.nf.test.snap
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
@@ -3,17 +3,12 @@ nextflow_process {
     name "Test Process UNTAR"
     script "../main.nf"
     process "UNTAR"
-
     tag "modules"
     tag "modules_nfcore"
     tag "untar"
-
     test("test_untar") {
 
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
                 input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ]
@@ -33,9 +28,6 @@ nextflow_process {
     test("test_untar_onlyfiles") {
 
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
                 input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ]

diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
@@ -22,9 +22,6 @@ nextflow_workflow {
                 input[1] = []
                 """
             }
-            params {
-                outdir = "output"
-            }
         }
 
         then {