Skip to content

Commit 04cebb5

Browse files
drpatelhdrpatelh
authored
Merge branch 'dev' into nf-core-template-merge-2.6
2 parents b11f984 + 4721317 commit 04cebb5

File tree

98 files changed

+284
-225
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

98 files changed

+284
-225
lines changed

‎CHANGELOG.md‎

Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,14 @@
33
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
44
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
55

6+
## [Unpublished Version / DEV]
7+
8+
### Enhancements & fixes
9+
10+
- Update modules to latest restructuring on nf-core/modules
11+
12+
### Parameters
13+
614
## [[3.9](https://github.com/nf-core/rnaseq/releases/tag/3.9)] - 2022-09-30
715

816
### Enhancements & fixes

‎modules.json‎

Lines changed: 167 additions & 165 deletions
Original file line numberDiff line numberDiff line change
@@ -2,172 +2,174 @@
22
"name": "nf-core/rnaseq",
33
"homePage": "https://github.com/nf-core/rnaseq",
44
"repos": {
5-
"nf-core/modules": {
6-
"git_url": "https://github.com/nf-core/modules.git",
5+
"https://github.com/nf-core/modules.git": {
76
"modules": {
8-
"bbmap/bbsplit": {
9-
"branch": "master",
10-
"git_sha": "848ee9a215d02d80be033bfa60881700f2bd914c"
11-
},
12-
"cat/fastq": {
13-
"branch": "master",
14-
"git_sha": "e9bc33485e420b51cfbed3cf63ac7463cd5739d3"
15-
},
16-
"custom/dumpsoftwareversions": {
17-
"branch": "master",
18-
"git_sha": "82501fe6d0d12614db67751d30af98d16e63dc59"
19-
},
20-
"custom/getchromsizes": {
21-
"branch": "master",
22-
"git_sha": "213403187932dbbdd936a04474cc8cd8abae7a08"
23-
},
24-
"fastqc": {
25-
"branch": "master",
26-
"git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
27-
},
28-
"gffread": {
29-
"branch": "master",
30-
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
31-
},
32-
"gunzip": {
33-
"branch": "master",
34-
"git_sha": "90aef30f432332bdf0ce9f4b9004aa5d5c4960bb"
35-
},
36-
"hisat2/align": {
37-
"branch": "master",
38-
"git_sha": "4eed099a12a7d586ce830a662a33a9df5bd67a24"
39-
},
40-
"hisat2/build": {
41-
"branch": "master",
42-
"git_sha": "4eed099a12a7d586ce830a662a33a9df5bd67a24"
43-
},
44-
"hisat2/extractsplicesites": {
45-
"branch": "master",
46-
"git_sha": "4eed099a12a7d586ce830a662a33a9df5bd67a24"
47-
},
48-
"picard/markduplicates": {
49-
"branch": "master",
50-
"git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
51-
},
52-
"preseq/lcextrap": {
53-
"branch": "master",
54-
"git_sha": "90aef30f432332bdf0ce9f4b9004aa5d5c4960bb"
55-
},
56-
"qualimap/rnaseq": {
57-
"branch": "master",
58-
"git_sha": "82501fe6d0d12614db67751d30af98d16e63dc59"
59-
},
60-
"rsem/calculateexpression": {
61-
"branch": "master",
62-
"git_sha": "1b5d3f5ac2ae61ee35dece20a2aeb8018b6438ce"
63-
},
64-
"rsem/preparereference": {
65-
"branch": "master",
66-
"git_sha": "1b5d3f5ac2ae61ee35dece20a2aeb8018b6438ce"
67-
},
68-
"rseqc/bamstat": {
69-
"branch": "master",
70-
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
71-
},
72-
"rseqc/inferexperiment": {
73-
"branch": "master",
74-
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
75-
},
76-
"rseqc/innerdistance": {
77-
"branch": "master",
78-
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
79-
},
80-
"rseqc/junctionannotation": {
81-
"branch": "master",
82-
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
83-
},
84-
"rseqc/junctionsaturation": {
85-
"branch": "master",
86-
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
87-
},
88-
"rseqc/readdistribution": {
89-
"branch": "master",
90-
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
91-
},
92-
"rseqc/readduplication": {
93-
"branch": "master",
94-
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
95-
},
96-
"rseqc/tin": {
97-
"branch": "master",
98-
"git_sha": "4dbc166a7c30e963511fb5c9870fbcaa158a53a9"
99-
},
100-
"salmon/index": {
101-
"branch": "master",
102-
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
103-
},
104-
"salmon/quant": {
105-
"branch": "master",
106-
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
107-
},
108-
"samtools/flagstat": {
109-
"branch": "master",
110-
"git_sha": "bbb99cb8d679555cc01c98766de7869f83283545"
111-
},
112-
"samtools/idxstats": {
113-
"branch": "master",
114-
"git_sha": "f0a86eaf5bf6ca73c5571193edd00c25bfa308f5"
115-
},
116-
"samtools/index": {
117-
"branch": "master",
118-
"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
119-
},
120-
"samtools/sort": {
121-
"branch": "master",
122-
"git_sha": "d5d785b3d8b422cda9c6d84a23f629a8e9ff8cd8"
123-
},
124-
"samtools/stats": {
125-
"branch": "master",
126-
"git_sha": "f4eab7945952dc4934224309701a49913ea05ae6"
127-
},
128-
"sortmerna": {
129-
"branch": "master",
130-
"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
131-
},
132-
"star/align": {
133-
"branch": "master",
134-
"git_sha": "cd22a76c78b09f7837a5a75642774a4bf48c92ba"
135-
},
136-
"star/genomegenerate": {
137-
"branch": "master",
138-
"git_sha": "cd22a76c78b09f7837a5a75642774a4bf48c92ba"
139-
},
140-
"stringtie/stringtie": {
141-
"branch": "master",
142-
"git_sha": "47cc7a77bfa10c0aa6e6c393d09e895a85d1583e"
143-
},
144-
"subread/featurecounts": {
145-
"branch": "master",
146-
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
147-
},
148-
"trimgalore": {
149-
"branch": "master",
150-
"git_sha": "bfbdc4f79bb26bc698d30b74abd081db8af77f4d"
151-
},
152-
"ucsc/bedclip": {
153-
"branch": "master",
154-
"git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
155-
},
156-
"ucsc/bedgraphtobigwig": {
157-
"branch": "master",
158-
"git_sha": "90aef30f432332bdf0ce9f4b9004aa5d5c4960bb"
159-
},
160-
"umitools/dedup": {
161-
"branch": "master",
162-
"git_sha": "9d489648a7425fa18d8bed18935442c104d8733c"
163-
},
164-
"umitools/extract": {
165-
"branch": "master",
166-
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
167-
},
168-
"untar": {
169-
"branch": "master",
170-
"git_sha": "b63b9f752dc8e43fc70b0491aad5e0a270ab0e10"
7+
"nf-core": {
8+
"bbmap/bbsplit": {
9+
"branch": "master",
10+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
11+
},
12+
"cat/fastq": {
13+
"branch": "master",
14+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
15+
},
16+
"custom/dumpsoftwareversions": {
17+
"branch": "master",
18+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
19+
},
20+
"custom/getchromsizes": {
21+
"branch": "master",
22+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
23+
"patch": "modules/nf-core/custom/getchromsizes/custom-getchromsizes.diff"
24+
},
25+
"fastqc": {
26+
"branch": "master",
27+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
28+
},
29+
"gffread": {
30+
"branch": "master",
31+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
32+
},
33+
"gunzip": {
34+
"branch": "master",
35+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
36+
},
37+
"hisat2/align": {
38+
"branch": "master",
39+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
40+
},
41+
"hisat2/build": {
42+
"branch": "master",
43+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
44+
},
45+
"hisat2/extractsplicesites": {
46+
"branch": "master",
47+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
48+
},
49+
"picard/markduplicates": {
50+
"branch": "master",
51+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
52+
},
53+
"preseq/lcextrap": {
54+
"branch": "master",
55+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
56+
},
57+
"qualimap/rnaseq": {
58+
"branch": "master",
59+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
60+
},
61+
"rsem/calculateexpression": {
62+
"branch": "master",
63+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
64+
},
65+
"rsem/preparereference": {
66+
"branch": "master",
67+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
68+
},
69+
"rseqc/bamstat": {
70+
"branch": "master",
71+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
72+
},
73+
"rseqc/inferexperiment": {
74+
"branch": "master",
75+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
76+
},
77+
"rseqc/innerdistance": {
78+
"branch": "master",
79+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
80+
},
81+
"rseqc/junctionannotation": {
82+
"branch": "master",
83+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
84+
},
85+
"rseqc/junctionsaturation": {
86+
"branch": "master",
87+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
88+
},
89+
"rseqc/readdistribution": {
90+
"branch": "master",
91+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
92+
},
93+
"rseqc/readduplication": {
94+
"branch": "master",
95+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
96+
},
97+
"rseqc/tin": {
98+
"branch": "master",
99+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
100+
},
101+
"salmon/index": {
102+
"branch": "master",
103+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
104+
},
105+
"salmon/quant": {
106+
"branch": "master",
107+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
108+
},
109+
"samtools/flagstat": {
110+
"branch": "master",
111+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
112+
},
113+
"samtools/idxstats": {
114+
"branch": "master",
115+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
116+
},
117+
"samtools/index": {
118+
"branch": "master",
119+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
120+
},
121+
"samtools/sort": {
122+
"branch": "master",
123+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
124+
},
125+
"samtools/stats": {
126+
"branch": "master",
127+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
128+
},
129+
"sortmerna": {
130+
"branch": "master",
131+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
132+
},
133+
"star/align": {
134+
"branch": "master",
135+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
136+
},
137+
"star/genomegenerate": {
138+
"branch": "master",
139+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
140+
},
141+
"stringtie/stringtie": {
142+
"branch": "master",
143+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
144+
},
145+
"subread/featurecounts": {
146+
"branch": "master",
147+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
148+
},
149+
"trimgalore": {
150+
"branch": "master",
151+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
152+
},
153+
"ucsc/bedclip": {
154+
"branch": "master",
155+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
156+
},
157+
"ucsc/bedgraphtobigwig": {
158+
"branch": "master",
159+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
160+
},
161+
"umitools/dedup": {
162+
"branch": "master",
163+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
164+
},
165+
"umitools/extract": {
166+
"branch": "master",
167+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
168+
},
169+
"untar": {
170+
"branch": "master",
171+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
172+
}
171173
}
172174
}
173175
}

‎modules/nf-core/modules/bbmap/bbsplit/main.nf‎ renamed to ‎modules/nf-core/bbmap/bbsplit/main.nf‎

File renamed without changes.

‎modules/nf-core/modules/bbmap/bbsplit/meta.yml‎ renamed to ‎modules/nf-core/bbmap/bbsplit/meta.yml‎

File renamed without changes.

‎modules/nf-core/modules/cat/fastq/main.nf‎ renamed to ‎modules/nf-core/cat/fastq/main.nf‎

File renamed without changes.

‎modules/nf-core/modules/cat/fastq/meta.yml‎ renamed to ‎modules/nf-core/cat/fastq/meta.yml‎

File renamed without changes.

‎modules/nf-core/modules/custom/dumpsoftwareversions/main.nf‎ renamed to ‎modules/nf-core/custom/dumpsoftwareversions/main.nf‎

File renamed without changes.

‎modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml‎ renamed to ‎modules/nf-core/custom/dumpsoftwareversions/meta.yml‎

File renamed without changes.

‎modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py‎ renamed to ‎modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py‎

File renamed without changes.

‎modules/nf-core/custom/getchromsizes/custom-getchromsizes.diff‎

Lines changed: 23 additions & 0 deletions
Some generated files are not rendered by default. Learn more about customizing how changed files appear on GitHub.

0 commit comments

Comments
 (0)