diff --git a/modules/nf-core/bedtools/genomecov/tests/main.nf.test b/modules/nf-core/bedtools/genomecov/tests/main.nf.test index 13f043102..b8caa1e11 100644 --- a/modules/nf-core/bedtools/genomecov/tests/main.nf.test +++ b/modules/nf-core/bedtools/genomecov/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { process "BEDTOOLS_GENOMECOV" config "./nextflow.config" - test("sarscov2 - no scale") { when { process { diff --git a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test index f13f39fa4..878c05d16 100644 --- a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test +++ b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "CUSTOM_CATADDITIONALFASTA" - test("sarscov2 - fastq - gtf") { when { diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test b/modules/nf-core/custom/getchromsizes/tests/main.nf.test index 8a05aeaae..2dadc1a55 100644 --- a/modules/nf-core/custom/getchromsizes/tests/main.nf.test +++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "CUSTOM_GETCHROMSIZES" - test("test_custom_getchromsizes") { when { diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test b/modules/nf-core/custom/tx2gene/tests/main.nf.test index 2d45b7646..e56a0b8fe 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "CUSTOM_TX2GENE" - test("saccharomyces_cerevisiae - gtf") { setup { diff --git a/modules/nf-core/dupradar/tests/main.nf.test b/modules/nf-core/dupradar/tests/main.nf.test index d45cefcfe..60f8dfb7d 100644 --- a/modules/nf-core/dupradar/tests/main.nf.test +++ b/modules/nf-core/dupradar/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "DUPRADAR" - test("sarscov2 - bam - single_end") { config './nextflow.config' diff --git a/modules/nf-core/fq/subsample/tests/main.nf.test b/modules/nf-core/fq/subsample/tests/main.nf.test index a7880501b..13bb75945 100644 --- a/modules/nf-core/fq/subsample/tests/main.nf.test +++ b/modules/nf-core/fq/subsample/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "FQ_SUBSAMPLE" - test("test_fq_subsample_no_args") { config "./nextflow_no_args.config" when { diff --git a/modules/nf-core/gffread/tests/main.nf.test b/modules/nf-core/gffread/tests/main.nf.test index 6d7c063ef..e03820f4d 100644 --- a/modules/nf-core/gffread/tests/main.nf.test +++ b/modules/nf-core/gffread/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "GFFREAD" - test("sarscov2-gff3-gtf") { config "./nextflow.config" diff --git a/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test b/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test index 37eb8b1f5..375f65357 100644 --- a/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test +++ b/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test @@ -5,7 +5,6 @@ nextflow_process { process "RSEQC_INFEREXPERIMENT" config "./nextflow.config" - test("sarscov2 - [[meta] - bam] - bed") { when { diff --git a/modules/nf-core/rseqc/innerdistance/tests/main.nf.test b/modules/nf-core/rseqc/innerdistance/tests/main.nf.test index 633d27d12..e54036f8a 100644 --- a/modules/nf-core/rseqc/innerdistance/tests/main.nf.test +++ b/modules/nf-core/rseqc/innerdistance/tests/main.nf.test @@ -5,7 +5,6 @@ nextflow_process { process "RSEQC_INNERDISTANCE" config "./nextflow.config" - test("sarscov2 - [[meta] - bam] - bed") { when { diff --git a/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test b/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test index b0e4eb86c..8a05bccab 100644 --- a/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test +++ b/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "RSEQC_JUNCTIONANNOTATION" - test("sarscov2 - paired end [bam]") { when { diff --git a/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test b/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test index 311125576..69d7f0c5d 100644 --- a/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test +++ b/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "RSEQC_JUNCTIONSATURATION" - test("sarscov2 paired-end [bam]") { when { diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index ea8a233de..6416ae127 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "SAMTOOLS_STATS" - test("bam") { when { diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test b/modules/nf-core/tximeta/tximport/tests/main.nf.test index d26e54100..782030fb8 100644 --- a/modules/nf-core/tximeta/tximport/tests/main.nf.test +++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "TXIMETA_TXIMPORT" - test("saccharomyces_cerevisiae - kallisto - gtf") { setup { diff --git a/modules/nf-core/umitools/dedup/tests/main.nf.test b/modules/nf-core/umitools/dedup/tests/main.nf.test index 4ba50c5fe..883e2d9d7 100644 --- a/modules/nf-core/umitools/dedup/tests/main.nf.test +++ b/modules/nf-core/umitools/dedup/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "UMITOOLS_DEDUP" - test("se - no stats") { config "./nextflow.config" diff --git a/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test b/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test index 4dfb522a3..105093505 100644 --- a/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test +++ b/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "UMITOOLS_PREPAREFORRSEM" - test("sarscov2 - bam") { when { diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test index 48dbcf2f0..f023a9f7d 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_workflow { script "../main.nf" workflow "BAM_MARKDUPLICATES_PICARD" - test("sarscov2 - bam") { when { diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test index eb944b7d5..053feffb6 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test @@ -181,7 +181,6 @@ nextflow_workflow { } } - test("skip_umi_extract") { when { @@ -675,7 +674,6 @@ nextflow_workflow { } } - test("skip_umi_extract - stub") { options "-stub" diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test index 352c62200..1043d06ad 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test @@ -6,7 +6,6 @@ nextflow_workflow { config './nextflow.config' - test("test single end read with UMI") { when { diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test index ce4ae964e..9c484b4aa 100644 --- a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test +++ b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test @@ -5,7 +5,6 @@ nextflow_workflow { workflow "QUANTIFY_PSEUDO_ALIGNMENT" - test("salmon") { setup {