From 6f5632c4e4fff5234f5ec1e54196a813fb427d1f Mon Sep 17 00:00:00 2001 From: Rob Syme Date: Sat, 9 Mar 2024 17:08:27 -0500 Subject: [PATCH 1/9] Initial attempt at nf-test for rsem_merge_counts --- .../rsem_merge_counts/tests/main.nf.test | 28 ++++++++++++ .../rsem_merge_counts/tests/main.nf.test.snap | 43 +++++++++++++++++++ .../local/rsem_merge_counts/tests/tags.yml | 2 + 3 files changed, 73 insertions(+) create mode 100644 modules/local/rsem_merge_counts/tests/main.nf.test create mode 100644 modules/local/rsem_merge_counts/tests/main.nf.test.snap create mode 100644 modules/local/rsem_merge_counts/tests/tags.yml diff --git a/modules/local/rsem_merge_counts/tests/main.nf.test b/modules/local/rsem_merge_counts/tests/main.nf.test new file mode 100644 index 000000000..6ceaf6d74 --- /dev/null +++ b/modules/local/rsem_merge_counts/tests/main.nf.test @@ -0,0 +1,28 @@ +nextflow_process { + + name "Test Process RSEM_MERGE_COUNTS" + script "../main.nf" + process "RSEM_MERGE_COUNTS" + tag "modules'" + tag "modules_local" + tag "rsem_merge_counts" + + test("Should run without failures") { + + when { + process { + """ + input[0] = file("${moduleTestDir}/data/genes/*") + input[1] = file("${moduleTestDir}/data/isoforms/*") + """ + } + } + + then { + assert process.success + assert snapshot(process.out).match() + } + + } + +} diff --git a/modules/local/rsem_merge_counts/tests/main.nf.test.snap b/modules/local/rsem_merge_counts/tests/main.nf.test.snap new file mode 100644 index 000000000..800263c1a --- /dev/null +++ b/modules/local/rsem_merge_counts/tests/main.nf.test.snap @@ -0,0 +1,43 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "rsem.merged.gene_counts.tsv:md5,7d1da94077dc2f90cfb2c793ca5b7446" + ], + "1": [ + "rsem.merged.gene_tpm.tsv:md5,39bad606eb012456bba1d995fe0feb5f" + ], + "2": [ + "rsem.merged.transcript_counts.tsv:md5,e40bba0aafc5904361513b3513c217ad" + ], + "3": [ + "rsem.merged.transcript_tpm.tsv:md5,abbaac45f9938716c58d604299ea284e" + ], + "4": [ + "versions.yml:md5,48ca3e12c91829af8019462b3f6aa29c" + ], + "counts_gene": [ + "rsem.merged.gene_counts.tsv:md5,7d1da94077dc2f90cfb2c793ca5b7446" + ], + "counts_transcript": [ + "rsem.merged.transcript_counts.tsv:md5,e40bba0aafc5904361513b3513c217ad" + ], + "tpm_gene": [ + "rsem.merged.gene_tpm.tsv:md5,39bad606eb012456bba1d995fe0feb5f" + ], + "tpm_transcript": [ + "rsem.merged.transcript_tpm.tsv:md5,abbaac45f9938716c58d604299ea284e" + ], + "versions": [ + "versions.yml:md5,48ca3e12c91829af8019462b3f6aa29c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-09T17:13:37.377348" + } +} \ No newline at end of file diff --git a/modules/local/rsem_merge_counts/tests/tags.yml b/modules/local/rsem_merge_counts/tests/tags.yml new file mode 100644 index 000000000..e1d8e23f0 --- /dev/null +++ b/modules/local/rsem_merge_counts/tests/tags.yml @@ -0,0 +1,2 @@ +RSEM_MERGE_COUNTS: + - "modules/local/rsem_merge_counts/**" From e71d687602fd6fbd269fa5902e2406f7d765fe84 Mon Sep 17 00:00:00 2001 From: Rob Syme Date: Sat, 9 Mar 2024 17:20:25 -0500 Subject: [PATCH 2/9] Include test data --- .../tests/data/genes/RAP1_IAA_30M_REP1.genes.results | 7 +++++++ .../tests/data/genes/RAP1_UNINDUCED_REP1.genes.results | 7 +++++++ .../tests/data/genes/RAP1_UNINDUCED_REP2.genes.results | 7 +++++++ .../tests/data/isoforms/RAP1_IAA_30M_REP1.isoforms.results | 7 +++++++ .../data/isoforms/RAP1_UNINDUCED_REP1.isoforms.results | 7 +++++++ .../data/isoforms/RAP1_UNINDUCED_REP2.isoforms.results | 7 +++++++ 6 files changed, 42 insertions(+) create mode 100644 modules/local/rsem_merge_counts/tests/data/genes/RAP1_IAA_30M_REP1.genes.results create mode 100644 modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP1.genes.results create mode 100644 modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP2.genes.results create mode 100644 modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_IAA_30M_REP1.isoforms.results create mode 100644 modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP1.isoforms.results create mode 100644 modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP2.isoforms.results diff --git a/modules/local/rsem_merge_counts/tests/data/genes/RAP1_IAA_30M_REP1.genes.results b/modules/local/rsem_merge_counts/tests/data/genes/RAP1_IAA_30M_REP1.genes.results new file mode 100644 index 000000000..29232f4ef --- /dev/null +++ b/modules/local/rsem_merge_counts/tests/data/genes/RAP1_IAA_30M_REP1.genes.results @@ -0,0 +1,7 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +Gfp_transgene Gfp_transgene 729.00 562.01 0.00 0.00 0.00 +HRA1 HRA1 564.00 397.05 0.00 0.00 0.00 +YAL001C YAL001C 3483.00 3316.01 55.00 762.38 490.51 +YAL002W YAL002W 3825.00 3658.01 34.00 427.23 274.88 +YAL003W YAL003W 621.00 454.02 616.00 62363.08 40124.02 +YAL004W YAL004W 648.00 481.02 1.00 95.56 61.48 diff --git a/modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP1.genes.results b/modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP1.genes.results new file mode 100644 index 000000000..247455005 --- /dev/null +++ b/modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP1.genes.results @@ -0,0 +1,7 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +Gfp_transgene Gfp_transgene 729.00 630.96 0.00 0.00 0.00 +HRA1 HRA1 564.00 465.96 0.00 0.00 0.00 +YAL001C YAL001C 3483.00 3384.96 69.00 937.05 581.61 +YAL002W YAL002W 3825.00 3726.96 30.00 370.03 229.67 +YAL003W YAL003W 621.00 522.96 798.00 70145.06 43537.87 +YAL004W YAL004W 648.00 549.96 0.00 0.00 0.00 diff --git a/modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP2.genes.results b/modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP2.genes.results new file mode 100644 index 000000000..79ce88374 --- /dev/null +++ b/modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP2.genes.results @@ -0,0 +1,7 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +Gfp_transgene Gfp_transgene 729.00 630.86 0.00 0.00 0.00 +HRA1 HRA1 564.00 465.86 0.00 0.00 0.00 +YAL001C YAL001C 3483.00 3384.86 110.00 783.22 460.39 +YAL002W YAL002W 3825.00 3726.86 81.00 523.81 307.91 +YAL003W YAL003W 621.00 522.86 1673.00 77115.22 45329.76 +YAL004W YAL004W 648.00 549.86 0.00 0.00 0.00 diff --git a/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_IAA_30M_REP1.isoforms.results b/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_IAA_30M_REP1.isoforms.results new file mode 100644 index 000000000..80c4bb9c3 --- /dev/null +++ b/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_IAA_30M_REP1.isoforms.results @@ -0,0 +1,7 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +Gfp_transgene Gfp_transgene 729 562.01 0.00 0.00 0.00 0.00 +HRA1 HRA1 564 397.05 0.00 0.00 0.00 0.00 +YAL001C YAL001C 3483 3316.01 55.00 762.38 490.51 100.00 +YAL002W YAL002W 3825 3658.01 34.00 427.23 274.88 100.00 +YAL003W YAL003W 621 454.02 616.00 62363.08 40124.02 100.00 +YAL004W YAL004W 648 481.02 1.00 95.56 61.48 100.00 diff --git a/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP1.isoforms.results b/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP1.isoforms.results new file mode 100644 index 000000000..24db5e716 --- /dev/null +++ b/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP1.isoforms.results @@ -0,0 +1,7 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +Gfp_transgene Gfp_transgene 729 630.96 0.00 0.00 0.00 0.00 +HRA1 HRA1 564 465.96 0.00 0.00 0.00 0.00 +YAL001C YAL001C 3483 3384.96 69.00 937.05 581.61 100.00 +YAL002W YAL002W 3825 3726.96 30.00 370.03 229.67 100.00 +YAL003W YAL003W 621 522.96 798.00 70145.06 43537.87 100.00 +YAL004W YAL004W 648 549.96 0.00 0.00 0.00 0.00 diff --git a/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP2.isoforms.results b/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP2.isoforms.results new file mode 100644 index 000000000..19d5bde86 --- /dev/null +++ b/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP2.isoforms.results @@ -0,0 +1,7 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +Gfp_transgene Gfp_transgene 729 630.86 0.00 0.00 0.00 0.00 +HRA1 HRA1 564 465.86 0.00 0.00 0.00 0.00 +YAL001C YAL001C 3483 3384.86 110.00 783.22 460.39 100.00 +YAL002W YAL002W 3825 3726.86 81.00 523.81 307.91 100.00 +YAL003W YAL003W 621 522.86 1673.00 77115.22 45329.76 100.00 +YAL004W YAL004W 648 549.86 0.00 0.00 0.00 0.00 From 0ad06dc503007a87e2b7d4a4aa0d7b789fe3d21f Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 11 Mar 2024 12:24:54 +0100 Subject: [PATCH 3/9] Update modules/local/rsem_merge_counts/tests/main.nf.test Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> --- modules/local/rsem_merge_counts/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/rsem_merge_counts/tests/main.nf.test b/modules/local/rsem_merge_counts/tests/main.nf.test index 6ceaf6d74..1019ec08a 100644 --- a/modules/local/rsem_merge_counts/tests/main.nf.test +++ b/modules/local/rsem_merge_counts/tests/main.nf.test @@ -3,7 +3,7 @@ nextflow_process { name "Test Process RSEM_MERGE_COUNTS" script "../main.nf" process "RSEM_MERGE_COUNTS" - tag "modules'" + tag "modules" tag "modules_local" tag "rsem_merge_counts" From 6e5c91d12c22bee24d8b53b6c39dad7ee0701885 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 11 Mar 2024 12:22:20 +0100 Subject: [PATCH 4/9] data to github --- .../tests/data/genes/RAP1_IAA_30M_REP1.genes.results | 7 ------- .../tests/data/genes/RAP1_UNINDUCED_REP1.genes.results | 7 ------- .../tests/data/genes/RAP1_UNINDUCED_REP2.genes.results | 7 ------- .../tests/data/isoforms/RAP1_IAA_30M_REP1.isoforms.results | 7 ------- .../data/isoforms/RAP1_UNINDUCED_REP1.isoforms.results | 7 ------- .../data/isoforms/RAP1_UNINDUCED_REP2.isoforms.results | 7 ------- 6 files changed, 42 deletions(-) delete mode 100644 modules/local/rsem_merge_counts/tests/data/genes/RAP1_IAA_30M_REP1.genes.results delete mode 100644 modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP1.genes.results delete mode 100644 modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP2.genes.results delete mode 100644 modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_IAA_30M_REP1.isoforms.results delete mode 100644 modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP1.isoforms.results delete mode 100644 modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP2.isoforms.results diff --git a/modules/local/rsem_merge_counts/tests/data/genes/RAP1_IAA_30M_REP1.genes.results b/modules/local/rsem_merge_counts/tests/data/genes/RAP1_IAA_30M_REP1.genes.results deleted file mode 100644 index 29232f4ef..000000000 --- a/modules/local/rsem_merge_counts/tests/data/genes/RAP1_IAA_30M_REP1.genes.results +++ /dev/null @@ -1,7 +0,0 @@ -gene_id transcript_id(s) length effective_length expected_count TPM FPKM -Gfp_transgene Gfp_transgene 729.00 562.01 0.00 0.00 0.00 -HRA1 HRA1 564.00 397.05 0.00 0.00 0.00 -YAL001C YAL001C 3483.00 3316.01 55.00 762.38 490.51 -YAL002W YAL002W 3825.00 3658.01 34.00 427.23 274.88 -YAL003W YAL003W 621.00 454.02 616.00 62363.08 40124.02 -YAL004W YAL004W 648.00 481.02 1.00 95.56 61.48 diff --git a/modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP1.genes.results b/modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP1.genes.results deleted file mode 100644 index 247455005..000000000 --- a/modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP1.genes.results +++ /dev/null @@ -1,7 +0,0 @@ -gene_id transcript_id(s) length effective_length expected_count TPM FPKM -Gfp_transgene Gfp_transgene 729.00 630.96 0.00 0.00 0.00 -HRA1 HRA1 564.00 465.96 0.00 0.00 0.00 -YAL001C YAL001C 3483.00 3384.96 69.00 937.05 581.61 -YAL002W YAL002W 3825.00 3726.96 30.00 370.03 229.67 -YAL003W YAL003W 621.00 522.96 798.00 70145.06 43537.87 -YAL004W YAL004W 648.00 549.96 0.00 0.00 0.00 diff --git a/modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP2.genes.results b/modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP2.genes.results deleted file mode 100644 index 79ce88374..000000000 --- a/modules/local/rsem_merge_counts/tests/data/genes/RAP1_UNINDUCED_REP2.genes.results +++ /dev/null @@ -1,7 +0,0 @@ -gene_id transcript_id(s) length effective_length expected_count TPM FPKM -Gfp_transgene Gfp_transgene 729.00 630.86 0.00 0.00 0.00 -HRA1 HRA1 564.00 465.86 0.00 0.00 0.00 -YAL001C YAL001C 3483.00 3384.86 110.00 783.22 460.39 -YAL002W YAL002W 3825.00 3726.86 81.00 523.81 307.91 -YAL003W YAL003W 621.00 522.86 1673.00 77115.22 45329.76 -YAL004W YAL004W 648.00 549.86 0.00 0.00 0.00 diff --git a/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_IAA_30M_REP1.isoforms.results b/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_IAA_30M_REP1.isoforms.results deleted file mode 100644 index 80c4bb9c3..000000000 --- a/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_IAA_30M_REP1.isoforms.results +++ /dev/null @@ -1,7 +0,0 @@ -transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct -Gfp_transgene Gfp_transgene 729 562.01 0.00 0.00 0.00 0.00 -HRA1 HRA1 564 397.05 0.00 0.00 0.00 0.00 -YAL001C YAL001C 3483 3316.01 55.00 762.38 490.51 100.00 -YAL002W YAL002W 3825 3658.01 34.00 427.23 274.88 100.00 -YAL003W YAL003W 621 454.02 616.00 62363.08 40124.02 100.00 -YAL004W YAL004W 648 481.02 1.00 95.56 61.48 100.00 diff --git a/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP1.isoforms.results b/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP1.isoforms.results deleted file mode 100644 index 24db5e716..000000000 --- a/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP1.isoforms.results +++ /dev/null @@ -1,7 +0,0 @@ -transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct -Gfp_transgene Gfp_transgene 729 630.96 0.00 0.00 0.00 0.00 -HRA1 HRA1 564 465.96 0.00 0.00 0.00 0.00 -YAL001C YAL001C 3483 3384.96 69.00 937.05 581.61 100.00 -YAL002W YAL002W 3825 3726.96 30.00 370.03 229.67 100.00 -YAL003W YAL003W 621 522.96 798.00 70145.06 43537.87 100.00 -YAL004W YAL004W 648 549.96 0.00 0.00 0.00 0.00 diff --git a/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP2.isoforms.results b/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP2.isoforms.results deleted file mode 100644 index 19d5bde86..000000000 --- a/modules/local/rsem_merge_counts/tests/data/isoforms/RAP1_UNINDUCED_REP2.isoforms.results +++ /dev/null @@ -1,7 +0,0 @@ -transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct -Gfp_transgene Gfp_transgene 729 630.86 0.00 0.00 0.00 0.00 -HRA1 HRA1 564 465.86 0.00 0.00 0.00 0.00 -YAL001C YAL001C 3483 3384.86 110.00 783.22 460.39 100.00 -YAL002W YAL002W 3825 3726.86 81.00 523.81 307.91 100.00 -YAL003W YAL003W 621 522.86 1673.00 77115.22 45329.76 100.00 -YAL004W YAL004W 648 549.86 0.00 0.00 0.00 0.00 From 089d9afe9f5c5a0ef25e370431575396d91b3dc5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 11 Mar 2024 12:27:46 +0100 Subject: [PATCH 5/9] fix path --- modules/local/rsem_merge_counts/tests/main.nf.test | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/rsem_merge_counts/tests/main.nf.test b/modules/local/rsem_merge_counts/tests/main.nf.test index 1019ec08a..5ae5aa68b 100644 --- a/modules/local/rsem_merge_counts/tests/main.nf.test +++ b/modules/local/rsem_merge_counts/tests/main.nf.test @@ -12,8 +12,8 @@ nextflow_process { when { process { """ - input[0] = file("${moduleTestDir}/data/genes/*") - input[1] = file("${moduleTestDir}/data/isoforms/*") + input[0] = file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/*", checkIfExists: true) + input[1] = file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/*", checkIfExists: true) """ } } From 5ac549f422834c039e95bf96e43a392c59cf31e1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 12 Mar 2024 11:53:26 +0100 Subject: [PATCH 6/9] collect input files --- modules/local/rsem_merge_counts/tests/main.nf.test | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/modules/local/rsem_merge_counts/tests/main.nf.test b/modules/local/rsem_merge_counts/tests/main.nf.test index 5ae5aa68b..0962a79b5 100644 --- a/modules/local/rsem_merge_counts/tests/main.nf.test +++ b/modules/local/rsem_merge_counts/tests/main.nf.test @@ -12,8 +12,16 @@ nextflow_process { when { process { """ - input[0] = file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/*", checkIfExists: true) - input[1] = file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/*", checkIfExists: true) + input[0] = Channel.of([ + file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/RAP1_IAA_30M_REP1.genes.results", checkIfExists: true), + file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/RAP1_UNINDUCED_REP1.genes.results", checkIfExists: true), + file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/RAP1_UNINDUCED_REP2.genes.results", checkIfExists: true) + ]).collect() + input[1] =Channel.of([ + file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_IAA_30M_REP1.isoforms.results", checkIfExists: true), + file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_UNINDUCED_REP1.isoforms.results", checkIfExists: true), + file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_UNINDUCED_REP2.isoforms.results", checkIfExists: true) + ]).collect() """ } } From 0f90900714a4c992c289a10153b3ece889d4f004 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 12 Mar 2024 11:58:31 +0100 Subject: [PATCH 7/9] Update modules/local/rsem_merge_counts/tests/main.nf.test Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> --- modules/local/rsem_merge_counts/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/rsem_merge_counts/tests/main.nf.test b/modules/local/rsem_merge_counts/tests/main.nf.test index 0962a79b5..e6a3ea91e 100644 --- a/modules/local/rsem_merge_counts/tests/main.nf.test +++ b/modules/local/rsem_merge_counts/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_process { file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/RAP1_UNINDUCED_REP1.genes.results", checkIfExists: true), file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/RAP1_UNINDUCED_REP2.genes.results", checkIfExists: true) ]).collect() - input[1] =Channel.of([ + input[1] = Channel.of([ file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_IAA_30M_REP1.isoforms.results", checkIfExists: true), file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_UNINDUCED_REP1.isoforms.results", checkIfExists: true), file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_UNINDUCED_REP2.isoforms.results", checkIfExists: true) From be63894880ff1f7d8a120e009f06d01f0423a816 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 12 Mar 2024 11:59:37 +0100 Subject: [PATCH 8/9] forgot to commit this file deletion --- modules/local/rsem_merge_counts/tests/tags.yml | 2 -- 1 file changed, 2 deletions(-) delete mode 100644 modules/local/rsem_merge_counts/tests/tags.yml diff --git a/modules/local/rsem_merge_counts/tests/tags.yml b/modules/local/rsem_merge_counts/tests/tags.yml deleted file mode 100644 index e1d8e23f0..000000000 --- a/modules/local/rsem_merge_counts/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -RSEM_MERGE_COUNTS: - - "modules/local/rsem_merge_counts/**" From 49d8fff0bc627beb9902a7b7c14dc96bc2710165 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 12 Mar 2024 12:16:20 +0100 Subject: [PATCH 9/9] Update modules/local/rsem_merge_counts/tests/main.nf.test --- modules/local/rsem_merge_counts/tests/main.nf.test | 3 --- 1 file changed, 3 deletions(-) diff --git a/modules/local/rsem_merge_counts/tests/main.nf.test b/modules/local/rsem_merge_counts/tests/main.nf.test index e6a3ea91e..9bb1caeb2 100644 --- a/modules/local/rsem_merge_counts/tests/main.nf.test +++ b/modules/local/rsem_merge_counts/tests/main.nf.test @@ -3,9 +3,6 @@ nextflow_process { name "Test Process RSEM_MERGE_COUNTS" script "../main.nf" process "RSEM_MERGE_COUNTS" - tag "modules" - tag "modules_local" - tag "rsem_merge_counts" test("Should run without failures") {