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--tools null -> --tools false
1 parent 0454fa1 commit c535870

14 files changed

+63
-61
lines changed

‎tests/intervals.nf.test

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ nextflow_pipeline {
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def test_scenario = [
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[
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name: "-profile test --intervals genome.multi_intervals.bed --tools null --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools",
12+
name: "-profile test --intervals genome.multi_intervals.bed --tools false --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools",
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params: [
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intervals: modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed",
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nucleotides_per_second: 20,
@@ -19,15 +19,15 @@ nextflow_pipeline {
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]
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],
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[
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name: "-profile test --no_intervals --tools null --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools",
22+
name: "-profile test --no_intervals --tools false --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools",
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params: [
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no_intervals: true,
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skip_tools: 'baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools',
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tools: null
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]
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],
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[
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name: "-profile test --intervals false --save_reference --tools null --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools",
30+
name: "-profile test --intervals false --save_reference --tools false --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools",
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params: [
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intervals: false,
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save_reference: true,
@@ -36,7 +36,7 @@ nextflow_pipeline {
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]
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],
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[
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name: "-profile test --intervals genome.multi_intervals.bed --tools null --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools -stub",
39+
name: "-profile test --intervals genome.multi_intervals.bed --tools false --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools -stub",
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params: [
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intervals: modules_testdata_base_path + "/genomics/homo_sapiens/genome/genome.multi_intervals.bed",
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nucleotides_per_second: 20,
@@ -47,7 +47,7 @@ nextflow_pipeline {
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stub: true
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],
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[
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name: "-profile test --no_intervals --tools null --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools -stub",
50+
name: "-profile test --no_intervals --tools false --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools -stub",
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params: [
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no_intervals: true,
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skip_tools: 'baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools',
@@ -56,7 +56,7 @@ nextflow_pipeline {
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stub: true
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],
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[
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name: "-profile test --intervals false --save_reference --tools null --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools -stub",
59+
name: "-profile test --intervals false --save_reference --tools false --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools -stub",
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params: [
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intervals: false,
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save_reference: true,

‎tests/intervals.nf.test.snap

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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{
2-
"-profile test --intervals false --save_reference --tools null --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools": {
2+
"-profile test --intervals false --save_reference --tools false --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools": {
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"content": [
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10,
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{
@@ -79,7 +79,7 @@
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},
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"timestamp": "2025-06-12T14:05:08.486696871"
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},
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"-profile test --intervals genome.multi_intervals.bed --tools null --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools": {
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"-profile test --intervals genome.multi_intervals.bed --tools false --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools": {
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"content": [
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10,
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{
@@ -134,7 +134,7 @@
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},
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"timestamp": "2025-06-12T14:02:08.414807739"
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},
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"-profile test --no_intervals --tools null --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools": {
137+
"-profile test --no_intervals --tools false --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools": {
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"content": [
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7,
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{
@@ -186,7 +186,7 @@
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},
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"timestamp": "2025-06-12T14:03:37.066714747"
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},
189-
"-profile test --no_intervals --tools null --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools -stub": {
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"-profile test --no_intervals --tools false --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools -stub": {
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"content": [
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{
@@ -232,7 +232,7 @@
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},
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"timestamp": "2025-07-02T11:53:00.073428657"
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},
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"-profile test --intervals false --save_reference --tools null --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools -stub": {
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"-profile test --intervals false --save_reference --tools false --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools -stub": {
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"content": [
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{
@@ -296,7 +296,7 @@
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},
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"timestamp": "2025-07-02T11:53:44.394696186"
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},
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"-profile test --intervals genome.multi_intervals.bed --tools null --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools -stub": {
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"-profile test --intervals genome.multi_intervals.bed --tools false --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools -stub": {
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"content": [
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{

‎tests/lane_integer.nf.test

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ nextflow_pipeline {
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def test_scenario = [
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[
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name: "-profile test --input tests/csv/3.0/fastq_single_integer_lane.csv --tools null --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools",
12+
name: "-profile test --input tests/csv/3.0/fastq_single_integer_lane.csv --tools false --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools",
1313
params: [
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input: "${projectDir}/tests/csv/3.0/fastq_single_integer_lane.csv",
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tools: null,

‎tests/lane_integer.nf.test.snap

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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{
2-
"-profile test --input tests/csv/3.0/fastq_single_integer_lane.csv --tools null --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools": {
2+
"-profile test --input tests/csv/3.0/fastq_single_integer_lane.csv --tools false --skip_tools baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools": {
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"content": [
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{

‎tests/preprocessing_umi.nf.test

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -9,15 +9,15 @@ nextflow_pipeline {
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def test_scenario = [
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[
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name: "-profile test --input tests/csv/3.0/fastq_umi.csv --umi_read_structure '+T 7M1S+T' --tools null",
12+
name: "-profile test --input tests/csv/3.0/fastq_umi.csv --umi_read_structure '+T 7M1S+T' --tools false",
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params: [
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input: "${projectDir}/tests/csv/3.0/fastq_umi.csv",
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tools: null,
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umi_read_structure: '+T 7M1S+T'
1717
]
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],
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[
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name: "-profile test --input tests/csv/3.0/fastq_umi.csv --umi_read_structure '+T 7M1S+T' --tools null --aligner sentieon-bwamem",
20+
name: "-profile test --input tests/csv/3.0/fastq_umi.csv --umi_read_structure '+T 7M1S+T' --tools false --aligner sentieon-bwamem",
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params: [
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input: "${projectDir}/tests/csv/3.0/fastq_umi.csv",
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tools: null,
@@ -28,7 +28,7 @@ nextflow_pipeline {
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stdout: "sentieon-bwamem is currently not compatible with FGBio UMI handling. Please choose a different aligner."
2929
],
3030
[
31-
name: "-profile test --input tests/csv/3.0/fastq_umi.csv --umi_read_structure '+T 7M1S+T' --tools null --aligner parabricks",
31+
name: "-profile test --input tests/csv/3.0/fastq_umi.csv --umi_read_structure '+T 7M1S+T' --tools false --aligner parabricks",
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params: [
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input: "${projectDir}/tests/csv/3.0/fastq_umi.csv",
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tools: null,

‎tests/preprocessing_umi.nf.test.snap

Lines changed: 28 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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{
2-
"-profile test --input tests/csv/3.0/fastq_umi.csv --umi_read_structure '+T 7M1S+T' --tools null": {
2+
"-profile test --input tests/csv/3.0/fastq_umi.csv --umi_read_structure '+T 7M1S+T'": {
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"content": [
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{
@@ -14,7 +14,7 @@
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"samtools": 1.21
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},
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"CALLUMICONSENSUS": {
17-
"fgbio": "2.4.0"
17+
"fgbio": "2.5.21"
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},
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"CAT_FASTQ": {
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"cat": 9.5
@@ -32,7 +32,7 @@
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"fastqc": "0.12.1"
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},
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"FASTQTOBAM": {
35-
"fgbio": "2.4.0"
35+
"fgbio": "2.5.21"
3636
},
3737
"GATK4_APPLYBQSR": {
3838
"gatk4": "4.6.1.0"
@@ -48,7 +48,7 @@
4848
"samtools": 1.21
4949
},
5050
"GROUPREADSBYUMI": {
51-
"fgbio": "2.4.0"
51+
"fgbio": "2.5.21"
5252
},
5353
"INDEX_CRAM": {
5454
"samtools": 1.21
@@ -252,7 +252,8 @@
252252
"reports/samtools/test/test.md.cram.stats",
253253
"reports/samtools/test/test.recal.cram.stats",
254254
"reports/umi",
255-
"reports/umi/test-test_L1_umi-grouped_histogram.txt"
255+
"reports/umi/test-test_L1_umi-grouped_histogram.txt",
256+
"reports/umi/test-test_L1_umi-grouped_read-metrics.txt"
256257
],
257258
[
258259
"fastqc-status-check-heatmap.txt:md5,92fcedba625d8394492d1ef6e2eb64f0",
@@ -266,41 +267,42 @@
266267
"fastqc_sequence_counts_plot.txt:md5,1a4aab87f1bd4fd9f69cabef40f5e5ed",
267268
"fastqc_sequence_duplication_levels_plot.txt:md5,72e6366160d000a2990b2bbd321300a7",
268269
"fastqc_sequence_length_distribution_plot.txt:md5,7c07faf0c0b90613cdc82a9f09bc1f19",
269-
"mosdepth-coverage-per-contig-single.txt:md5,800ad271050c46d24bf53c0f8bdf7b6e",
270-
"mosdepth-cumcoverage-dist-id.txt:md5,3c526ec6da433233b419bdbdd19a1b56",
271-
"mosdepth_perchrom.txt:md5,800ad271050c46d24bf53c0f8bdf7b6e",
270+
"mosdepth-coverage-per-contig-single.txt:md5,fc8d90478e230b3cbad16ef68ede3a62",
271+
"mosdepth-cumcoverage-dist-id.txt:md5,7985d3196b234be9907f6c417c4fe0df",
272+
"mosdepth_perchrom.txt:md5,fc8d90478e230b3cbad16ef68ede3a62",
272273
"multiqc_citations.txt:md5,7d0b4b866fa577272c48a1f3ad72e75d",
273274
"multiqc_fastqc.txt:md5,0ca2cba4204d9076a1eb17596379d10c",
274275
"picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
275276
"picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
276277
"picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
277-
"samtools-stats-dp.txt:md5,4d27768d75a69a61daf23bf5efe17687",
278-
"samtools_alignment_plot.txt:md5,3c2a882852a7ffe06610c9027f0a312a",
279-
"test.md.mosdepth.global.dist.txt:md5,09d22913aa50a0207f97a3f85b182c6e",
280-
"test.md.mosdepth.region.dist.txt:md5,61676a4a3668c0e84eb0f56dc6bda1ae",
281-
"test.md.mosdepth.summary.txt:md5,9bbea5e4d213a51f501c2aadff8d4526",
282-
"test.md.regions.bed.gz:md5,e24c18ad56e54376c41fdaacec372f9e",
283-
"test.md.regions.bed.gz.csi:md5,d0713716f63ac573f4a3385733e9a537",
284-
"test.recal.mosdepth.global.dist.txt:md5,09d22913aa50a0207f97a3f85b182c6e",
285-
"test.recal.mosdepth.region.dist.txt:md5,61676a4a3668c0e84eb0f56dc6bda1ae",
286-
"test.recal.mosdepth.summary.txt:md5,9bbea5e4d213a51f501c2aadff8d4526",
287-
"test.recal.regions.bed.gz:md5,e24c18ad56e54376c41fdaacec372f9e",
288-
"test.recal.regions.bed.gz.csi:md5,d0713716f63ac573f4a3385733e9a537",
289-
"test-test_L1_umi-grouped_histogram.txt:md5,85292e9acb83edf17110dce17be27f44"
278+
"samtools-stats-dp.txt:md5,7409b0ac85933f622b30f6b53777e894",
279+
"samtools_alignment_plot.txt:md5,60b8f1d48124a8f28b06dc0d15ca4d59",
280+
"test.md.mosdepth.global.dist.txt:md5,34135a9f55bc3ed522c38fe0cce2d89a",
281+
"test.md.mosdepth.region.dist.txt:md5,11dc4683f9038de1938b4874e02974d6",
282+
"test.md.mosdepth.summary.txt:md5,d6cda5af0f2bf21973e256cf198aa47a",
283+
"test.md.regions.bed.gz:md5,2e0526a15f549024c6a7d99232543642",
284+
"test.md.regions.bed.gz.csi:md5,5c556fe6462be13681267bb28257b654",
285+
"test.recal.mosdepth.global.dist.txt:md5,34135a9f55bc3ed522c38fe0cce2d89a",
286+
"test.recal.mosdepth.region.dist.txt:md5,11dc4683f9038de1938b4874e02974d6",
287+
"test.recal.mosdepth.summary.txt:md5,d6cda5af0f2bf21973e256cf198aa47a",
288+
"test.recal.regions.bed.gz:md5,2e0526a15f549024c6a7d99232543642",
289+
"test.recal.regions.bed.gz.csi:md5,5c556fe6462be13681267bb28257b654",
290+
"test-test_L1_umi-grouped_histogram.txt:md5,85292e9acb83edf17110dce17be27f44",
291+
"test-test_L1_umi-grouped_read-metrics.txt:md5,cb2aecfe82357aa06e091d69b4606b9e"
290292
],
291293
[
292-
"test-test_L1_umi-consensus.bam:md5,18d420720f72366289d3a324f4552522"
294+
"test-test_L1_umi-consensus.bam:md5,f11107c297c012c78616d7de965a0255"
293295
],
294296
[
295-
"test.md.cram:md5,2d0c176fed158d84a061b69e1947994c",
296-
"test.recal.cram:md5,6927569ca52dbba512d27f8742bc6aae"
297+
"test.md.cram:md5,9287aa93e5575923930765531544150",
298+
"test.recal.cram:md5,9287aa93e5575923930765531544150"
297299
],
298300
"No VCF files"
299301
],
300302
"meta": {
301303
"nf-test": "0.9.2",
302-
"nextflow": "25.04.3"
304+
"nextflow": "25.04.6"
303305
},
304-
"timestamp": "2025-06-16T10:56:22.096321902"
306+
"timestamp": "2025-08-18T11:54:00.612320399"
305307
}
306308
}

‎tests/sentieon.nf.test

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@@ -8,7 +8,7 @@ nextflow_pipeline {
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def test_scenario = [
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[
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name: "-profile test --aligner sentieon-bwamem --tools null -stub",
11+
name: "-profile test --aligner sentieon-bwamem --tools false -stub",
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params: [
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aligner: "sentieon-bwamem",
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tools: ''

‎tests/sentieon.nf.test.snap

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{
2-
"-profile test --aligner sentieon-bwamem --tools null -stub": {
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"-profile test --aligner sentieon-bwamem --tools false -stub": {
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{

‎tests/start_from_markduplicates.nf.test

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Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ nextflow_pipeline {
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def test_scenario = [
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[
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name: "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools null",
12+
name: "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools false",
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params: [
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input: "${projectDir}/tests/csv/3.0/mapped_single_bam.csv",
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step: 'markduplicates',
@@ -18,7 +18,7 @@ nextflow_pipeline {
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]
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],
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[
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name: "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --tools null",
21+
name: "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --tools false",
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params: [
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modules_testdata_base_path: 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/',
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input: "${projectDir}/tests/csv/3.0/mapped_single_bam.csv",
@@ -27,7 +27,7 @@ nextflow_pipeline {
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]
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],
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[
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name: "-profile test --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --tools null",
30+
name: "-profile test --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --tools false",
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params: [
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modules_testdata_base_path: 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/',
3333
input: "${projectDir}/tests/csv/3.0/mapped_single_cram.csv",
@@ -37,7 +37,7 @@ nextflow_pipeline {
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]
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],
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[
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name: "-profile test --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --tools null",
40+
name: "-profile test --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --tools false",
4141
params: [
4242
modules_testdata_base_path: 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/',
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input: "${projectDir}/tests/csv/3.0/mapped_single_cram.csv",

‎tests/start_from_markduplicates.nf.test.snap

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@@ -1,5 +1,5 @@
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{
2-
"-profile test --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --tools null": {
2+
"-profile test --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --tools false": {
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"content": [
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{
@@ -175,7 +175,7 @@
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},
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"timestamp": "2025-06-16T13:03:47.021313698"
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},
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"-profile test --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --tools null": {
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"-profile test --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --tools false": {
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"content": [
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{
@@ -351,7 +351,7 @@
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},
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"timestamp": "2025-06-16T13:06:07.261866128"
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},
354-
"-profile test --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --tools null": {
354+
"-profile test --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --tools false": {
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"content": [
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{
@@ -499,7 +499,7 @@
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},
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"timestamp": "2025-06-16T13:04:53.758263352"
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},
502-
"-profile test --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools null": {
502+
"-profile test --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools false": {
503503
"content": [
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12,
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{

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