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Merge pull request #1335 from maxulysse/stubs_everywhere
Adding stubs at all level
2 parents 75995bf + 1b34d1e commit ad43736

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‎.github/workflows/ci.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ on:
55

66
env:
77
NXF_ANSI_LOG: false
8-
NFT_VER: "0.8.4"
8+
NFT_VER: "0.9.0"
99
NFT_WORKDIR: "~"
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NFT_DIFF: "pdiff"
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NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"

‎CHANGELOG.md‎

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Original file line numberDiff line numberDiff line change
@@ -102,6 +102,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
102102
- [PR #1330](https://github.com/nf-core/rnaseq/pull/1330) - Update all nf-core/modules and subworkflows
103103
- [PR #1331](https://github.com/nf-core/rnaseq/pull/1331) - Adding stubs for local modules
104104
- [PR #1334](https://github.com/nf-core/rnaseq/pull/1334) - Update all nf-core/modules and subworkflows with stubs
105+
- [PR #1335](https://github.com/nf-core/rnaseq/pull/1335) - Adding stubs at all levels
105106
- [PR #1336](https://github.com/nf-core/rnaseq/pull/1334) - Use nf-core/setup-nf-test to install nf-test from cache during CI/CD
106107
- [PR #1340](https://github.com/nf-core/rnaseq/pull/1340) - Remove out-of-date Azure specific guidance
107108
- [PR #1341](https://github.com/nf-core/rnaseq/pull/1341) - Add rename in the MultiQC report for samples without techreps
@@ -137,6 +138,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
137138
| `samtools` | 1.17 | 1.20 |
138139
| `sortmerna` | 4.3.4 | 4.3.6 |
139140
| `umi_tools` | 1.14 | 1.15 |
141+
| `untar` | 1.3 | 1.34 |
140142

141143
> **NB:** Dependency has been **updated** if both old and new version information is present.
142144
>

‎modules.json‎

Lines changed: 37 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
"nf-core": {
88
"bbmap/bbsplit": {
99
"branch": "master",
10-
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
10+
"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
1111
"installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
1212
},
1313
"bedtools/genomecov": {
@@ -17,22 +17,22 @@
1717
},
1818
"cat/fastq": {
1919
"branch": "master",
20-
"git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e",
20+
"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
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"installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
2222
},
2323
"custom/catadditionalfasta": {
2424
"branch": "master",
25-
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
25+
"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
2626
"installed_by": ["modules"]
2727
},
2828
"custom/getchromsizes": {
2929
"branch": "master",
30-
"git_sha": "41a4135c502b42ede663af87efa70a96ecbd7cb9",
30+
"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
3131
"installed_by": ["modules"]
3232
},
3333
"custom/tx2gene": {
3434
"branch": "master",
35-
"git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9",
35+
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
3636
"installed_by": ["modules", "quantify_pseudo_alignment"]
3737
},
3838
"dupradar": {
@@ -42,12 +42,12 @@
4242
},
4343
"fastp": {
4444
"branch": "master",
45-
"git_sha": "b90b5cd93149a1b3be263d916c7234fe0708a71c",
45+
"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
4646
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
4747
},
4848
"fastqc": {
4949
"branch": "master",
50-
"git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
50+
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
5151
"installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
5252
},
5353
"fq/subsample": {
@@ -62,7 +62,7 @@
6262
},
6363
"gunzip": {
6464
"branch": "master",
65-
"git_sha": "a7231cbccb86535529e33859e05d19ac93f3ea04",
65+
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
6666
"installed_by": ["modules"]
6767
},
6868
"hisat2/align": {
@@ -82,12 +82,12 @@
8282
},
8383
"kallisto/index": {
8484
"branch": "master",
85-
"git_sha": "de5811dd9ca15af1e131806001bcaae909e42021",
85+
"git_sha": "fbe341e9af0bb98533757f536b26d38507d31724",
8686
"installed_by": ["modules"]
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},
8888
"kallisto/quant": {
8989
"branch": "master",
90-
"git_sha": "de5811dd9ca15af1e131806001bcaae909e42021",
90+
"git_sha": "fbe341e9af0bb98533757f536b26d38507d31724",
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"installed_by": ["modules", "quantify_pseudo_alignment"]
9292
},
9393
"multiqc": {
@@ -97,8 +97,9 @@
9797
},
9898
"picard/markduplicates": {
9999
"branch": "master",
100-
"git_sha": "1943aa60f7490c3d6740e8872e6e69122ccc8087",
101-
"installed_by": ["bam_markduplicates_picard"]
100+
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
101+
"installed_by": ["bam_markduplicates_picard"],
102+
"patch": "modules/nf-core/picard/markduplicates/picard-markduplicates.diff"
102103
},
103104
"preseq/lcextrap": {
104105
"branch": "master",
@@ -107,7 +108,7 @@
107108
},
108109
"qualimap/rnaseq": {
109110
"branch": "master",
110-
"git_sha": "6b0e4fe14ca1b12e131f64608f0bbaf36fd11451",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
111112
"installed_by": ["modules"]
112113
},
113114
"rsem/calculateexpression": {
@@ -172,17 +173,17 @@
172173
},
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"samtools/flagstat": {
174175
"branch": "master",
175-
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
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"installed_by": ["bam_stats_samtools"]
177178
},
178179
"samtools/idxstats": {
179180
"branch": "master",
180-
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
181182
"installed_by": ["bam_stats_samtools"]
182183
},
183184
"samtools/index": {
184185
"branch": "master",
185-
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
186+
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
186187
"installed_by": [
187188
"bam_dedup_stats_samtools_umitools",
188189
"bam_markduplicates_picard",
@@ -191,12 +192,12 @@
191192
},
192193
"samtools/sort": {
193194
"branch": "master",
194-
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
195+
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
195196
"installed_by": ["bam_sort_stats_samtools"]
196197
},
197198
"samtools/stats": {
198199
"branch": "master",
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"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
200+
"git_sha": "1fe379cf6e6c1e6fa5e32bcbeefea0f1e874dac6",
200201
"installed_by": ["bam_stats_samtools"]
201202
},
202203
"sortmerna": {
@@ -206,17 +207,17 @@
206207
},
207208
"star/align": {
208209
"branch": "master",
209-
"git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
210+
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
210211
"installed_by": ["modules"]
211212
},
212213
"star/genomegenerate": {
213214
"branch": "master",
214-
"git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
215+
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
215216
"installed_by": ["modules"]
216217
},
217218
"stringtie/stringtie": {
218219
"branch": "master",
219-
"git_sha": "b1b959609bda44341120aed1766329909f54b8d0",
220+
"git_sha": "c789476080a150f87066ca3ed42a622339a26c0b",
220221
"installed_by": ["modules"]
221222
},
222223
"subread/featurecounts": {
@@ -226,7 +227,7 @@
226227
},
227228
"summarizedexperiment/summarizedexperiment": {
228229
"branch": "master",
229-
"git_sha": "31751460f9ce9552846e13fdeec6953dcb47132d",
230+
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
230231
"installed_by": ["modules", "quantify_pseudo_alignment"]
231232
},
232233
"trimgalore": {
@@ -246,12 +247,12 @@
246247
},
247248
"ucsc/bedgraphtobigwig": {
248249
"branch": "master",
249-
"git_sha": "7c75d01997236f61b9b77399d9933cb36041f2c3",
250+
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
250251
"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
251252
},
252253
"umitools/dedup": {
253254
"branch": "master",
254-
"git_sha": "3bd4f34e3093c2a16e6a8eefc22242b9b94641db",
255+
"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
255256
"installed_by": ["bam_dedup_stats_samtools_umitools"]
256257
},
257258
"umitools/extract": {
@@ -266,7 +267,7 @@
266267
},
267268
"untar": {
268269
"branch": "master",
269-
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
270+
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
270271
"installed_by": ["modules"]
271272
}
272273
}
@@ -275,27 +276,27 @@
275276
"nf-core": {
276277
"bam_dedup_stats_samtools_umitools": {
277278
"branch": "master",
278-
"git_sha": "8f2062e7b4185590fb9f43c275381a31a6544fc0",
279+
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
279280
"installed_by": ["subworkflows"]
280281
},
281282
"bam_markduplicates_picard": {
282283
"branch": "master",
283-
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
284+
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
284285
"installed_by": ["subworkflows"]
285286
},
286287
"bam_rseqc": {
287288
"branch": "master",
288-
"git_sha": "9eb22e4d3f28c274b7c498a1564581377349a242",
289+
"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
289290
"installed_by": ["subworkflows"]
290291
},
291292
"bam_sort_stats_samtools": {
292293
"branch": "master",
293-
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
294+
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
294295
"installed_by": ["fastq_align_hisat2"]
295296
},
296297
"bam_stats_samtools": {
297298
"branch": "master",
298-
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
299+
"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
299300
"installed_by": [
300301
"bam_dedup_stats_samtools_umitools",
301302
"bam_markduplicates_picard",
@@ -304,22 +305,22 @@
304305
},
305306
"bedgraph_bedclip_bedgraphtobigwig": {
306307
"branch": "master",
307-
"git_sha": "a4bceac1aecee5aa0a5dbc601baf0e2e61013fb2",
308+
"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
308309
"installed_by": ["subworkflows"]
309310
},
310311
"fastq_align_hisat2": {
311312
"branch": "master",
312-
"git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e",
313+
"git_sha": "c789476080a150f87066ca3ed42a622339a26c0b",
313314
"installed_by": ["subworkflows"]
314315
},
315316
"fastq_fastqc_umitools_fastp": {
316317
"branch": "master",
317-
"git_sha": "db35d26edeafacf9906a517827df621a29adc13d",
318+
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
318319
"installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
319320
},
320321
"fastq_fastqc_umitools_trimgalore": {
321322
"branch": "master",
322-
"git_sha": "cb6defa0834eda9d6d3f967e981c819fc3e257bf",
323+
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
323324
"installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
324325
},
325326
"fastq_qc_trim_filter_setstrandedness": {
@@ -329,12 +330,12 @@
329330
},
330331
"fastq_subsample_fq_salmon": {
331332
"branch": "master",
332-
"git_sha": "727232afb8294b53dd9d05bfe469b70cce1675bb",
333+
"git_sha": "fbe341e9af0bb98533757f536b26d38507d31724",
333334
"installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
334335
},
335336
"quantify_pseudo_alignment": {
336337
"branch": "master",
337-
"git_sha": "5d095e8413da1f4c72b7d07ce87f75c09482486f",
338+
"git_sha": "fbe341e9af0bb98533757f536b26d38507d31724",
338339
"installed_by": ["subworkflows"]
339340
},
340341
"utils_nextflow_pipeline": {

‎modules/local/deseq2_qc/main.nf‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -63,16 +63,16 @@ process DESEQ2_QC {
6363
def label_lower = args2.toLowerCase()
6464
prefix = task.ext.prefix ?: "deseq2"
6565
"""
66-
mkdir size_factors
6766
touch ${label_lower}.pca.vals_mqc.tsv
6867
touch ${label_lower}.sample.dists_mqc.tsv
69-
touch ${prefix}.plots.pdf
7068
touch ${prefix}.dds.RData
7169
touch ${prefix}.pca.vals.txt
70+
touch ${prefix}.plots.pdf
7271
touch ${prefix}.sample.dists.txt
7372
touch R_sessionInfo.log
74-
touch size_factors/${prefix}.size_factors.RData
7573
74+
mkdir size_factors
75+
touch size_factors/${prefix}.size_factors.RData
7676
for i in `head $counts -n 1 | cut -f3-`;
7777
do
7878
touch size_factors/\${i}.size_factors.RData

‎modules/local/star_align_igenomes/main.nf‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -76,6 +76,8 @@ process STAR_ALIGN_IGENOMES {
7676
stub:
7777
def prefix = task.ext.prefix ?: "${meta.id}"
7878
"""
79+
echo "" | gzip > ${prefix}.unmapped_1.fastq.gz
80+
echo "" | gzip > ${prefix}.unmapped_2.fastq.gz
7981
touch ${prefix}Xd.out.bam
8082
touch ${prefix}.Log.final.out
8183
touch ${prefix}.Log.out
@@ -84,8 +86,6 @@ process STAR_ALIGN_IGENOMES {
8486
touch ${prefix}.toTranscriptome.out.bam
8587
touch ${prefix}.Aligned.unsort.out.bam
8688
touch ${prefix}.Aligned.sortedByCoord.out.bam
87-
touch ${prefix}.unmapped_1.fastq.gz
88-
touch ${prefix}.unmapped_2.fastq.gz
8989
touch ${prefix}.tab
9090
touch ${prefix}.SJ.out.tab
9191
touch ${prefix}.ReadsPerGene.out.tab

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