Remove --outdir definition in nf-tests for workflows

drpatelh · drpatelh · commit cbe835e4906e · 2024-02-28T12:15:59.000Z
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
@@ -20,9 +20,6 @@ nextflow_workflow {
                 input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035")
                 """
             }
-            params {
-                outdir = "$outputDir"
-            }
         }
 
         then {
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -21,7 +21,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 nf_core_pipeline = "rnaseq"
                 ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5"
                 sample_mapping_fields = "run_accession,library_layout"
diff --git a/workflows/sra/tests/sra_download_method_aspera.nf.test b/workflows/sra/tests/sra_download_method_aspera.nf.test
@@ -21,7 +21,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 download_method = 'aspera'
             }
         }
diff --git a/workflows/sra/tests/sra_download_method_sratools.nf.test b/workflows/sra/tests/sra_download_method_sratools.nf.test
@@ -21,7 +21,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 download_method = 'sratools'
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -21,7 +21,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 nf_core_pipeline = "atacseq"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -21,7 +21,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 nf_core_pipeline = "rnaseq"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -21,7 +21,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 nf_core_pipeline = "taxprofiler"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -21,7 +21,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 nf_core_pipeline = "viralrecon"
             }
         }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -20,7 +20,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 skip_fastq_download = true
             }
         }

Original file line number	Diff line number	Diff line change
`@@ -20,9 +20,6 @@ nextflow_workflow {`
`20`	`20`	`input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035")`
`21`	`21`	`"""`
`22`	`22`	`}`
`23`		`- params {`
`24`		`- outdir = "$outputDir"`
`25`		`- }`
`26`	`23`	`}`
`27`	`24`
`28`	`25`	`then {`
Original file line number	Diff line number	Diff line change
`@@ -21,7 +21,6 @@ nextflow_workflow {`
`21`	`21`	`"""`
`22`	`22`	`}`
`23`	`23`	`params {`
`24`		`- outdir = "$outputDir"`
`25`	`24`	`nf_core_pipeline = "rnaseq"`
`26`	`25`	`ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5"`
`27`	`26`	`sample_mapping_fields = "run_accession,library_layout"`
Original file line number	Diff line number	Diff line change
`@@ -20,7 +20,6 @@ nextflow_workflow {`
`20`	`20`	`"""`
`21`	`21`	`}`
`22`	`22`	`params {`
`23`		`- outdir = "$outputDir"`
`24`	`23`	`skip_fastq_download = true`
`25`	`24`	`}`
`26`	`25`	`}`