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maxulyssemaxulysse
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do not snapshot the bam
1 parent 997fb25 commit 6866c24

9 files changed

+9
-87
lines changed

‎tests/.nftignore‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ kallisto/*/kallisto_quant.log
55
kallisto/*/run_info.json
66
kallisto/kallisto.*
77
{multiqc,multiqc/**}/multiqc_report.html
8-
{multiqc,multiqc/**}/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt
8+
{multiqc,multiqc/**}/multiqc_report_data/fastqc_{raw,trimmed}_top_overrepresented_sequences_table.txt
99
{multiqc,multiqc/**}/multiqc_report_data/junction_saturation_known.txt
1010
{multiqc,multiqc/**}/multiqc_report_data/junction_saturation_novel.txt
1111
{multiqc,multiqc/**}/multiqc_report_data/kallisto_alignment.txt

‎tests/default.nf.test‎

Lines changed: 1 addition & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -16,8 +16,6 @@ nextflow_pipeline {
1616
def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
1717
// stable_path: All files in ${params.outdir}/ with stable content
1818
def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
19-
// bam_files: All bam files
20-
def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
2119
assertAll(
2220
{ assert workflow.success},
2321
{ assert snapshot(
@@ -28,9 +26,7 @@ nextflow_pipeline {
2826
// All stable path name, with a relative path
2927
stable_name,
3028
// All files with stable contents
31-
stable_path,
32-
// All bam files
33-
bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] }
29+
stable_path
3430
).match() }
3531
)
3632
}

‎tests/default.nf.test.snap‎

Lines changed: 1 addition & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -1299,7 +1299,6 @@
12991299
"fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
13001300
"fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c",
13011301
"fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
1302-
"fastqc_raw_top_overrepresented_sequences_table.txt:md5,43d63c7c7f038becc6b5ef164b2e5f71",
13031302
"fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
13041303
"fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
13051304
"fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
@@ -1455,28 +1454,6 @@
14551454
"i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
14561455
"i_data.ctab:md5,041edee3193df311f621c09f4991892b",
14571456
"tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
1458-
],
1459-
[
1460-
[
1461-
"RAP1_IAA_30M_REP1.markdup.sorted.bam",
1462-
"289857e4f0b6c753038917027f5d88bd"
1463-
],
1464-
[
1465-
"RAP1_UNINDUCED_REP1.markdup.sorted.bam",
1466-
"6c1e33dc619c8ad4799f7cf39dcf2d2f"
1467-
],
1468-
[
1469-
"RAP1_UNINDUCED_REP2.markdup.sorted.bam",
1470-
"bbd70318082b935fce75ee323d5dba50"
1471-
],
1472-
[
1473-
"WT_REP1.markdup.sorted.bam",
1474-
"255c653935697006430033367caa9669"
1475-
],
1476-
[
1477-
"WT_REP2.markdup.sorted.bam",
1478-
"fce663681eba11bdd48c67d4281d7d4d"
1479-
]
14801457
]
14811458
],
14821459
"meta": {
@@ -1485,4 +1462,4 @@
14851462
},
14861463
"timestamp": "2024-10-10T09:48:14.477734"
14871464
}
1488-
}
1465+
}

‎tests/featurecounts_group_type.nf.test‎

Lines changed: 1 addition & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -17,8 +17,6 @@ nextflow_pipeline {
1717
def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
1818
// stable_path: All files in ${params.outdir}/ with stable content
1919
def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
20-
// bam_files: All bam files
21-
def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
2220
assertAll(
2321
{ assert workflow.success},
2422
{ assert snapshot(
@@ -29,9 +27,7 @@ nextflow_pipeline {
2927
// All stable path name, with a relative path
3028
stable_name,
3129
// All files with stable contents
32-
stable_path,
33-
// All bam files
34-
bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] }
30+
stable_path
3531
).match() }
3632
)
3733
}

‎tests/featurecounts_group_type.nf.test.snap‎

Lines changed: 1 addition & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -1265,7 +1265,6 @@
12651265
"fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
12661266
"fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c",
12671267
"fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
1268-
"fastqc_raw_top_overrepresented_sequences_table.txt:md5,43d63c7c7f038becc6b5ef164b2e5f71",
12691268
"fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
12701269
"fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
12711270
"fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
@@ -1405,28 +1404,6 @@
14051404
"i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
14061405
"i_data.ctab:md5,041edee3193df311f621c09f4991892b",
14071406
"tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
1408-
],
1409-
[
1410-
[
1411-
"RAP1_IAA_30M_REP1.markdup.sorted.bam",
1412-
"76476167553ce185faf6fa44b01d34da"
1413-
],
1414-
[
1415-
"RAP1_UNINDUCED_REP1.markdup.sorted.bam",
1416-
"c3384e7240bc0291f4c6e3fb91f6cc82"
1417-
],
1418-
[
1419-
"RAP1_UNINDUCED_REP2.markdup.sorted.bam",
1420-
"1db43d2a4ad9d37865e0777bf943deaf"
1421-
],
1422-
[
1423-
"WT_REP1.markdup.sorted.bam",
1424-
"afa34b079825ffdcc260968053509ef3"
1425-
],
1426-
[
1427-
"WT_REP2.markdup.sorted.bam",
1428-
"fd478d307f2c27138b0ff003b904c481"
1429-
]
14301407
]
14311408
],
14321409
"meta": {
@@ -1435,4 +1412,4 @@
14351412
},
14361413
"timestamp": "2024-10-10T10:00:00.235948"
14371414
}
1438-
}
1415+
}

‎tests/hisat2.nf.test‎

Lines changed: 1 addition & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -17,8 +17,6 @@ nextflow_pipeline {
1717
def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
1818
// stable_path: All files in ${params.outdir}/ with stable content
1919
def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
20-
// bam_files: All bam files
21-
def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
2220
assertAll(
2321
{ assert workflow.success},
2422
{ assert snapshot(
@@ -29,9 +27,7 @@ nextflow_pipeline {
2927
// All stable path name, with a relative path
3028
stable_name,
3129
// All files with stable contents
32-
stable_path,
33-
// All bam files
34-
bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] }
30+
stable_path
3531
).match() }
3632
)
3733
}

‎tests/hisat2.nf.test.snap‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -761,7 +761,6 @@
761761
"multiqc/hisat2/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt",
762762
"multiqc/hisat2/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt",
763763
"multiqc/hisat2/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt",
764-
"multiqc/hisat2/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt",
765764
"multiqc/hisat2/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt",
766765
"multiqc/hisat2/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt",
767766
"multiqc/hisat2/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt",
@@ -1340,4 +1339,4 @@
13401339
},
13411340
"timestamp": "2024-10-10T10:25:14.209047"
13421341
}
1343-
}
1342+
}

‎tests/min_mapped_reads.nf.test‎

Lines changed: 1 addition & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -17,8 +17,6 @@ nextflow_pipeline {
1717
def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
1818
// stable_path: All files in ${params.outdir}/ with stable content
1919
def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
20-
// bam_files: All bam files
21-
def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
2220
assertAll(
2321
{ assert workflow.success},
2422
{ assert snapshot(
@@ -29,9 +27,7 @@ nextflow_pipeline {
2927
// All stable path name, with a relative path
3028
stable_name,
3129
// All files with stable contents
32-
stable_path,
33-
// All bam files
34-
bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] }
30+
stable_path
3531
).match() }
3632
)
3733
}

‎tests/min_mapped_reads.nf.test.snap‎

Lines changed: 1 addition & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -1039,7 +1039,6 @@
10391039
"fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
10401040
"fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c",
10411041
"fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
1042-
"fastqc_raw_top_overrepresented_sequences_table.txt:md5,43d63c7c7f038becc6b5ef164b2e5f71",
10431042
"fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
10441043
"fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
10451044
"fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
@@ -1170,20 +1169,6 @@
11701169
"i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
11711170
"i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e",
11721171
"tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
1173-
],
1174-
[
1175-
[
1176-
"RAP1_IAA_30M_REP1.markdup.sorted.bam",
1177-
"542a64613e641be18a172830f281b319"
1178-
],
1179-
[
1180-
"RAP1_UNINDUCED_REP1.markdup.sorted.bam",
1181-
"42765cd169f11cb21c4ca680b1f8f200"
1182-
],
1183-
[
1184-
"RAP1_UNINDUCED_REP2.markdup.sorted.bam",
1185-
"3146dc95e97f6b3036b046613bb5102f"
1186-
]
11871172
]
11881173
],
11891174
"meta": {
@@ -1286,4 +1271,4 @@
12861271
},
12871272
"timestamp": "2024-10-10T10:37:37.274627"
12881273
}
1289-
}
1274+
}

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