Skip to content

Commit e55e9ff

Browse files
ctunictuni
authored
Merge pull request #84 from Emeerdink/align_dev
STAR running and whole pipeline completing successfully :)
2 parents 2b2a188 + abb9ffb commit e55e9ff

File tree

116 files changed

+11541
-68
lines changed

Some content is hidden

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

116 files changed

+11541
-68
lines changed

‎conf/test.config‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@
1313
process {
1414
resourceLimits = [
1515
cpus: 4,
16-
memory: '15.GB',
16+
memory: '12.GB',
1717
time: '1.h'
1818
]
1919
}
@@ -39,6 +39,7 @@ params {
3939

4040
// Other parameters
4141
skip_bbsplit = false
42+
aligner = 'star'
4243
}
4344

4445
// When using RSEM, remove warning from STAR whilst building tiny indices

‎modules.json‎

Lines changed: 103 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -55,6 +55,11 @@
5555
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
5656
"installed_by": ["modules"]
5757
},
58+
"hisat2/align": {
59+
"branch": "master",
60+
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
61+
"installed_by": ["fastq_align_hisat2"]
62+
},
5863
"hisat2/build": {
5964
"branch": "master",
6065
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
@@ -90,26 +95,85 @@
9095
"git_sha": "85b5f8a0d9df9ce7587af50e2ee75b37c97515c6",
9196
"installed_by": ["fastq_subsample_fq_salmon"]
9297
},
98+
"samtools/flagstat": {
99+
"branch": "master",
100+
"git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
101+
"installed_by": ["bam_stats_samtools"]
102+
},
103+
"samtools/idxstats": {
104+
"branch": "master",
105+
"git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
106+
"installed_by": ["bam_stats_samtools"]
107+
},
108+
"samtools/index": {
109+
"branch": "master",
110+
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
111+
"installed_by": [
112+
"bam_dedup_stats_samtools_umicollapse",
113+
"bam_dedup_stats_samtools_umitools",
114+
"bam_sort_stats_samtools"
115+
]
116+
},
117+
"samtools/sort": {
118+
"branch": "master",
119+
"git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
120+
"installed_by": ["bam_dedup_umi", "bam_sort_stats_samtools"]
121+
},
122+
"samtools/stats": {
123+
"branch": "master",
124+
"git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
125+
"installed_by": ["bam_stats_samtools"]
126+
},
93127
"sortmerna": {
94128
"branch": "master",
95129
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
96130
"installed_by": ["fastq_qc_trim_filter_setstrandedness"]
97131
},
132+
"star/align": {
133+
"branch": "master",
134+
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
135+
"installed_by": ["fastq_align_star", "modules"]
136+
},
98137
"star/genomegenerate": {
99138
"branch": "master",
100139
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
101140
"installed_by": ["modules"]
102141
},
142+
"stringtie/merge": {
143+
"branch": "master",
144+
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
145+
"installed_by": ["modules"]
146+
},
147+
"stringtie/stringtie": {
148+
"branch": "master",
149+
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
150+
"installed_by": ["modules"]
151+
},
103152
"trimgalore": {
104153
"branch": "master",
105154
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
106155
"installed_by": ["fastq_fastqc_umitools_trimgalore"]
107156
},
157+
"umicollapse": {
158+
"branch": "master",
159+
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
160+
"installed_by": ["bam_dedup_stats_samtools_umicollapse"]
161+
},
162+
"umitools/dedup": {
163+
"branch": "master",
164+
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
165+
"installed_by": ["bam_dedup_stats_samtools_umitools"]
166+
},
108167
"umitools/extract": {
109168
"branch": "master",
110169
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
111170
"installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
112171
},
172+
"umitools/prepareforrsem": {
173+
"branch": "master",
174+
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
175+
"installed_by": ["bam_dedup_umi"]
176+
},
113177
"untar": {
114178
"branch": "master",
115179
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
@@ -119,6 +183,45 @@
119183
},
120184
"subworkflows": {
121185
"nf-core": {
186+
"bam_dedup_stats_samtools_umicollapse": {
187+
"branch": "master",
188+
"git_sha": "0b27602842d3d79fd0e8db79f4afa764967fc3d1",
189+
"installed_by": ["bam_dedup_umi"]
190+
},
191+
"bam_dedup_stats_samtools_umitools": {
192+
"branch": "master",
193+
"git_sha": "0b27602842d3d79fd0e8db79f4afa764967fc3d1",
194+
"installed_by": ["bam_dedup_umi"]
195+
},
196+
"bam_dedup_umi": {
197+
"branch": "master",
198+
"git_sha": "332fdceaada99b70d9a538db57430afb19566fe0",
199+
"installed_by": ["subworkflows"]
200+
},
201+
"bam_sort_stats_samtools": {
202+
"branch": "master",
203+
"git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
204+
"installed_by": ["bam_dedup_umi", "fastq_align_hisat2", "fastq_align_star"]
205+
},
206+
"bam_stats_samtools": {
207+
"branch": "master",
208+
"git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
209+
"installed_by": [
210+
"bam_dedup_stats_samtools_umicollapse",
211+
"bam_dedup_stats_samtools_umitools",
212+
"bam_sort_stats_samtools"
213+
]
214+
},
215+
"fastq_align_hisat2": {
216+
"branch": "master",
217+
"git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e",
218+
"installed_by": ["subworkflows"]
219+
},
220+
"fastq_align_star": {
221+
"branch": "master",
222+
"git_sha": "6a367612c2c27aa659293c656afa764361223db4",
223+
"installed_by": ["subworkflows"]
224+
},
122225
"fastq_fastqc_umitools_fastp": {
123226
"branch": "master",
124227
"git_sha": "51c21921e151011213e5cf553cf06e6657e77594",

‎modules/nf-core/hisat2/align/environment.yml‎

Lines changed: 8 additions & 0 deletions
Some generated files are not rendered by default. Learn more about customizing how changed files appear on GitHub.

‎modules/nf-core/hisat2/align/main.nf‎

Lines changed: 109 additions & 0 deletions
Some generated files are not rendered by default. Learn more about customizing how changed files appear on GitHub.

‎modules/nf-core/hisat2/align/meta.yml‎

Lines changed: 88 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)