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Don't snapshot logs
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@pinin4fjords
pinin4fjords committed Mar 7, 2024
1 parent d0676b2 commit 34d3abd
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Showing 2 changed files with 120 additions and 181 deletions.
26 changes: 23 additions & 3 deletions subworkflows/local/quantify_rsem/tests/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,11 +41,31 @@ nextflow_workflow {

then {
assertAll(
{ assert workflow.success},
{ assert snapshot(workflow.out).match()}
{ assert workflow.success },
{ assert snapshot(
workflow.out.counts_gene,
workflow.out.counts_transcript,
workflow.out.stat,
workflow.out.bam_star,
workflow.out.bam_genome,
workflow.out.bam_transcript,
workflow.out.counts_transcript,
workflow.out.bam,
workflow.out.bai,
workflow.out.csi,
workflow.out.stats,
workflow.out.flagstat,
workflow.out.idxstats,
workflow.out.merged_counts_gene,
workflow.out.merged_tpm_gene,
workflow.out.merged_counts_transcript,
workflow.out.merged_tpm_transcript,
workflow.out.versions
).match()
},
{ assert snapshot(file(workflow.out.logs[0][1]).name).match('logs') }
)
}

}

}
275 changes: 97 additions & 178 deletions subworkflows/local/quantify_rsem/tests/main.nf.test.snap
View file
Original file line number Diff line number Diff line change
@@ -1,191 +1,110 @@
{
"logs": {
"content": [
"test.log"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-03-07T18:25:31.476361"
},
"homo_sapiens": {
"content": [
{
"0": [
[
{
"id": "test",
"strandedness": "forward"
},
"test.genes.results:md5,c7ec226f76736ea805771e73553ae359"
]
],
"1": [
[
{
"id": "test",
"strandedness": "forward"
},
"test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8"
]
],
"10": [

],
"11": [

],
"12": [

],
"13": [
"rsem.merged.gene_counts.tsv:md5,f3b586000c97c89aec45360772e73df1"
],
"14": [
"rsem.merged.gene_tpm.tsv:md5,e6ae3dfa9913a7c15b705ec27c376212"
],
"15": [
"rsem.merged.transcript_counts.tsv:md5,235c002b811360183494a2aac74d1f5b"
],
"16": [
"rsem.merged.transcript_tpm.tsv:md5,d38f22667e3b8012f1d783b8d5159ccc"
],
"17": [
"versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9",
"versions.yml:md5,ae1676b60b6335fff8f1188288103a1c"
],
"2": [
[
{
"id": "test",
"strandedness": "forward"
},
[
"test.cnt:md5,76249e6b2f3c104f414aae596ba2c2f4",
"test.model:md5,a7a4bc1734918ef5848604e3362b83e2",
"test.theta:md5,de2e4490c98cc5383a86ae8225fd0a28"
]
]
],
"3": [
[
{
"id": "test",
"strandedness": "forward"
},
"test.log:md5,0854a613698cf8511b3b8db9ee9ad07e"
]
],
"4": [

],
"5": [

],
"6": [
[
{
"id": "test",
"strandedness": "forward"
},
"test.transcript.bam:md5,ed681d39f5700ffc74d6321525330d93"
]
],
"7": [

],
"8": [

],
"9": [

],
"bai": [

],
"bam": [

],
"bam_genome": [

],
"bam_star": [

],
"bam_transcript": [
[
{
"id": "test",
"strandedness": "forward"
},
"test.transcript.bam:md5,ed681d39f5700ffc74d6321525330d93"
]
],
"counts_gene": [
[
{
"id": "test",
"strandedness": "forward"
},
"test.genes.results:md5,c7ec226f76736ea805771e73553ae359"
]
],
"counts_transcript": [
[
{
"id": "test",
"strandedness": "forward"
},
"test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8"
]
],
"csi": [

],
"flagstat": [

],
"idxstats": [

],
"logs": [
[
{
"id": "test",
"strandedness": "forward"
},
"test.log:md5,0854a613698cf8511b3b8db9ee9ad07e"
]
],
"merged_counts_gene": [
"rsem.merged.gene_counts.tsv:md5,f3b586000c97c89aec45360772e73df1"
],
"merged_counts_transcript": [
"rsem.merged.transcript_counts.tsv:md5,235c002b811360183494a2aac74d1f5b"
],
"merged_tpm_gene": [
"rsem.merged.gene_tpm.tsv:md5,e6ae3dfa9913a7c15b705ec27c376212"
],
"merged_tpm_transcript": [
"rsem.merged.transcript_tpm.tsv:md5,d38f22667e3b8012f1d783b8d5159ccc"
],
"stat": [
[
[
{
"id": "test",
"strandedness": "forward"
},
"test.genes.results:md5,c7ec226f76736ea805771e73553ae359"
]
],
[
[
{
"id": "test",
"strandedness": "forward"
},
"test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8"
]
],
[
[
{
"id": "test",
"strandedness": "forward"
},
[
{
"id": "test",
"strandedness": "forward"
},
[
"test.cnt:md5,76249e6b2f3c104f414aae596ba2c2f4",
"test.model:md5,a7a4bc1734918ef5848604e3362b83e2",
"test.theta:md5,de2e4490c98cc5383a86ae8225fd0a28"
]
"test.cnt:md5,76249e6b2f3c104f414aae596ba2c2f4",
"test.model:md5,a7a4bc1734918ef5848604e3362b83e2",
"test.theta:md5,de2e4490c98cc5383a86ae8225fd0a28"
]
],
"stats": [

],
"versions": [
"versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9",
"versions.yml:md5,ae1676b60b6335fff8f1188288103a1c"
]
}
],
[

],
[

],
[
[
{
"id": "test",
"strandedness": "forward"
},
"test.transcript.bam:md5,ed681d39f5700ffc74d6321525330d93"
]
],
[
[
{
"id": "test",
"strandedness": "forward"
},
"test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8"
]
],
[

],
[

],
[

],
[

],
[

],
[

],
[
"rsem.merged.gene_counts.tsv:md5,f3b586000c97c89aec45360772e73df1"
],
[
"rsem.merged.gene_tpm.tsv:md5,e6ae3dfa9913a7c15b705ec27c376212"
],
[
"rsem.merged.transcript_counts.tsv:md5,235c002b811360183494a2aac74d1f5b"
],
[
"rsem.merged.transcript_tpm.tsv:md5,d38f22667e3b8012f1d783b8d5159ccc"
],
[
"versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9",
"versions.yml:md5,ae1676b60b6335fff8f1188288103a1c"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-03-07T17:50:58.226946"
"timestamp": "2024-03-07T18:15:03.001083"
}
}

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