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Fix module and workflow tests and snapshots
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@emi80
emi80 committed Jun 17, 2024
1 parent d07b425 commit 47ab4f2
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Showing 17 changed files with 70 additions and 180 deletions.
2 changes: 1 addition & 1 deletion tests/modules/bigwig/rgcrg/main.nf.test.snap
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Expand Up @@ -27,4 +27,4 @@
},
"timestamp": "2024-04-30T19:01:02.919082"
}
}
}
2 changes: 1 addition & 1 deletion tests/modules/bigwig/star/main.bigwig.nf.test.snap
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Expand Up @@ -31,4 +31,4 @@
},
"timestamp": "2024-04-25T12:34:53.753279"
}
}
}
2 changes: 1 addition & 1 deletion tests/modules/bigwig/star/main.signal.nf.test.snap
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Expand Up @@ -22,4 +22,4 @@
},
"timestamp": "2024-04-25T12:33:44.577831"
}
}
}
2 changes: 1 addition & 1 deletion tests/modules/contig/rgcrg/main.nf.test.snap
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Expand Up @@ -21,4 +21,4 @@
},
"timestamp": "2024-04-30T18:57:32.893994"
}
}
}
10 changes: 5 additions & 5 deletions tests/modules/inferExp/rseqc/main.nf.test.snap
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@@ -1,5 +1,5 @@
{
"Should infer strandedness from BAM (uncompressed annotation)": {
"Should infer strandedness from BAM (compressed annotation)": {
"content": [
{
"0": [
Expand All @@ -15,9 +15,9 @@
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-18T18:54:10.824148"
"timestamp": "2024-04-18T18:54:02.195879"
},
"Should infer strandedness from BAM (compressed annotation)": {
"Should infer strandedness from BAM (uncompressed annotation)": {
"content": [
{
"0": [
Expand All @@ -33,6 +33,6 @@
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-18T18:54:02.195879"
"timestamp": "2024-04-18T18:54:10.824148"
}
}
}
4 changes: 2 additions & 2 deletions tests/modules/mapping/gem/main.map.nf.test
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Expand Up @@ -27,7 +27,7 @@ nextflow_process {
}
process {
"""
def fastqs = file("${baseDir}/data/test1_*.fastq.gz")
def fastqs = file("${baseDir}/data/test1_*.fastq.gz").sort()
def qScore = fastq(fastqs[0]).qualityScore()
input[0] = file("${baseDir}/data/annotation.gtf.gz")
input[1] = index.out
Expand Down Expand Up @@ -56,7 +56,7 @@ nextflow_process {
}
process {
"""
def fastqs = file("${baseDir}/data/test1_*.fastq.gz")
def fastqs = file("${baseDir}/data/test1_*.fastq.gz").sort()
def qScore = fastq(fastqs[0]).qualityScore()
input[0] = file("${baseDir}/data/annotation.gtf")
input[1] = index.out
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2 changes: 1 addition & 1 deletion tests/modules/mapping/star/main.index.nf.test.snap
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Expand Up @@ -47,4 +47,4 @@
},
"timestamp": "2024-04-17T17:20:43.134729"
}
}
}
4 changes: 2 additions & 2 deletions tests/modules/mapping/star/main.map.nf.test
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Expand Up @@ -33,7 +33,7 @@ nextflow_process {
input[1] = index.out
input[2] = Channel.from(
[
[ "sample1", "test1", file("${baseDir}/data/test1_*.fastq.gz"), "fastq", ["fqRd1", "fqRd2"], '']
[ "sample1", "test1", file("${baseDir}/data/test1_*.fastq.gz").sort(), "fastq", ["fqRd1", "fqRd2"], '']
]
)
"""
Expand Down Expand Up @@ -67,7 +67,7 @@ nextflow_process {
input[1] = index.out
input[2] = Channel.from(
[
[ "sample1", "test1", file("${baseDir}/data/test1_*.fastq.gz"), "fastq", ["fqRd1", "fqRd2"], '']
[ "sample1", "test1", file("${baseDir}/data/test1_*.fastq.gz").sort(), "fastq", ["fqRd1", "fqRd2"], '']
]
)
"""
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6 changes: 3 additions & 3 deletions tests/modules/mapping/star/main.map.nf.test.snap
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Expand Up @@ -12,7 +12,7 @@
]
],
[

],
[
[
Expand Down Expand Up @@ -54,7 +54,7 @@
]
],
[

],
[
[
Expand Down Expand Up @@ -83,4 +83,4 @@
},
"timestamp": "2024-04-23T23:11:13.889531"
}
}
}
2 changes: 1 addition & 1 deletion tests/modules/mergeBam/sambamba/main.nf.test
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Expand Up @@ -16,7 +16,7 @@ nextflow_process {
process {
"""
input[0] = Channel.from([
[ "sample2", [ "test2", "test3" ], file("${baseDir}/data/test*/*toGenome_sorted.bam"), "bam", "GenomeAlignments", true]
[ "sample2", [ "test2", "test3" ], file("${baseDir}/data/test*/*toGenome_sorted.bam").sort(), "bam", "GenomeAlignments", true]
])
"""
}
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4 changes: 2 additions & 2 deletions tests/modules/mergeBam/sambamba/main.nf.test.snap
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Expand Up @@ -6,7 +6,7 @@
[
"sample2",
"test2:test3",
"sample2_m4_n10_toGenome.bam:md5,724ebe0d965d40decaa80c6b09e47ba5",
"sample2_m4_n10_toGenome.bam:md5,92d1c59a6e5b111f7a277135310415c2",
"bam",
"GenomeAlignments",
true
Expand All @@ -18,6 +18,6 @@
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-05-02T11:08:00.400122"
"timestamp": "2024-06-17T17:22:45.897345592"
}
}
2 changes: 1 addition & 1 deletion tests/modules/mergeBam/samtools/main.nf.test
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Expand Up @@ -16,7 +16,7 @@ nextflow_process {
process {
"""
input[0] = Channel.from([
[ "sample2", [ "test2", "test3" ], file("${baseDir}/data/test*/*toGenome_sorted.bam"), "bam", "GenomeAlignments", true]
[ "sample2", [ "test2", "test3" ], file("${baseDir}/data/test*/*toGenome_sorted.bam").sort() , "bam", "GenomeAlignments", true]
])
"""
}
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6 changes: 3 additions & 3 deletions tests/modules/mergeBam/samtools/main.nf.test.snap
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Expand Up @@ -6,7 +6,7 @@
[
"sample2",
"test2:test3",
"sample2_m4_n10_toGenome.bam:md5,1aafe9aacc6e403ed8a5466a30549c85",
"sample2_m4_n10_toGenome.bam:md5,9c721443896d97df3f2151ce5397c512",
"bam",
"GenomeAlignments",
true
Expand All @@ -16,8 +16,8 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.2"
},
"timestamp": "2024-05-02T11:27:59.686395"
"timestamp": "2024-06-17T16:44:46.900499"
}
}
55 changes: 0 additions & 55 deletions tests/modules/quantification/rsem/main.calculateExpression.nf.test.snap
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@@ -1,59 +1,4 @@
{
"Should quantify with RSEM (with credibility intervals)": {
"content": [
{
"0": [
[
"sample3",
"test3",
"sample3.isoforms.results:md5,a2ddfd7d7919830d69f941176ddff86f",
"tsv",
"TranscriptQuantifications",
true,
"MATE2_SENSE"
]
],
"1": [
[
"sample3",
"test3",
"sample3.genes.results:md5,568855cd154369988f0e9120660dcea6",
"tsv",
"GeneQuantifications",
true,
"MATE2_SENSE"
]
],
"genes": [
[
"sample3",
"test3",
"sample3.genes.results:md5,568855cd154369988f0e9120660dcea6",
"tsv",
"GeneQuantifications",
true,
"MATE2_SENSE"
]
],
"isoforms": [
[
"sample3",
"test3",
"sample3.isoforms.results:md5,a2ddfd7d7919830d69f941176ddff86f",
"tsv",
"TranscriptQuantifications",
true,
"MATE2_SENSE"
]
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-30T17:37:25.520162"
},
"Should quantify with RSEM converting the input BAM file": {
"content": [
{
Expand Down
4 changes: 2 additions & 2 deletions tests/workflows/mapping.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ nextflow_workflow {
input[1] = file("${baseDir}/data/annotation.gtf.gz")
input[2] = Channel.from(
[
[ "sample1", "test1", file("${baseDir}/data/test1_*.fastq.gz"), "fastq", ["fqRd1", "fqRd2"], '']
[ "sample1", "test1", file("${baseDir}/data/test1_*.fastq.gz").sort(), "fastq", ["fqRd1", "fqRd2"], '']
]
)
"""
Expand Down Expand Up @@ -59,7 +59,7 @@ nextflow_workflow {
input[1] = file("${baseDir}/data/annotation.gtf")
input[2] = Channel.from(
[
[ "sample1", "test1", file("${baseDir}/data/test1_*.fastq.gz"), "fastq", ["fqRd1", "fqRd2"], '']
[ "sample1", "test1", file("${baseDir}/data/test1_*.fastq.gz").sort(), "fastq", ["fqRd1", "fqRd2"], '']
]
)
"""
Expand Down
55 changes: 0 additions & 55 deletions tests/workflows/quantification/rsem.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,59 +1,4 @@
{
"Should run quantification with RSEM (with credibility intervals)": {
"content": [
{
"0": [
[
"sample3",
"test3",
"sample3.genes.results:md5,568855cd154369988f0e9120660dcea6",
"tsv",
"GeneQuantifications",
true,
"MATE2_SENSE"
]
],
"1": [
[
"sample3",
"test3",
"sample3.isoforms.results:md5,a2ddfd7d7919830d69f941176ddff86f",
"tsv",
"TranscriptQuantifications",
true,
"MATE2_SENSE"
]
],
"genes": [
[
"sample3",
"test3",
"sample3.genes.results:md5,568855cd154369988f0e9120660dcea6",
"tsv",
"GeneQuantifications",
true,
"MATE2_SENSE"
]
],
"isoforms": [
[
"sample3",
"test3",
"sample3.isoforms.results:md5,a2ddfd7d7919830d69f941176ddff86f",
"tsv",
"TranscriptQuantifications",
true,
"MATE2_SENSE"
]
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-30T17:55:23.922489"
},
"Should run quantification with RSEM": {
"content": [
{
Expand Down
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