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Move most of local modules to nf-core modules #521

Merged
merged 28 commits into from
Apr 27, 2022
Merged

Move most of local modules to nf-core modules #521

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3cd9b70
remove unused module
maxulysse Apr 14, 2022
8f0910d
code polishing for alignment_to_fastq
maxulysse Apr 19, 2022
528e5ab
code polishing
maxulysse Apr 19, 2022
53c88ca
local -> nf-core for collatefastq module
maxulysse Apr 20, 2022
1bf4b12
add bgzip decompress
maxulysse Apr 20, 2022
15a16b3
fix MODULE name
maxulysse Apr 20, 2022
6bcf24a
actually use the nf-core module that is already there
maxulysse Apr 20, 2022
af8a483
fully remove old files
maxulysse Apr 20, 2022
645d2b0
module samtools/bamtocram local -> nf-core
maxulysse Apr 25, 2022
d477de5
fix number of input channels
maxulysse Apr 25, 2022
de35065
Merge remote-tracking branch 'upstream/dev' into dev_modules_die_samt…
maxulysse Apr 25, 2022
4586a2e
remove unused module
maxulysse Apr 25, 2022
6c873b4
quick code polish
maxulysse Apr 25, 2022
b895d08
use nf-core samtools/index module instead of local
maxulysse Apr 25, 2022
a0b2ffc
fix output saving
maxulysse Apr 25, 2022
4212f75
fix syntax
maxulysse Apr 25, 2022
cddce67
publish out of mapping
maxulysse Apr 25, 2022
047038d
Merge remote-tracking branch 'upstream/dev' into dev_modules_die_samt…
maxulysse Apr 25, 2022
33bdc1c
fix merge bam after mapping (skip markduplicates
maxulysse Apr 26, 2022
9bcbc8f
fix input for INDEX_MERGE_BAM
maxulysse Apr 26, 2022
a1cd1e7
fix output for tests
maxulysse Apr 26, 2022
6b1ef51
Apply suggestions from code review
maxulysse Apr 26, 2022
2108b6a
code polish
maxulysse Apr 27, 2022
81d273e
revert back
maxulysse Apr 27, 2022
63074e8
move channel map/groupTuple logic from subworkflow to workflow
maxulysse Apr 27, 2022
ebbe0d1
Apply suggestions from code review
maxulysse Apr 27, 2022
c098b9c
code polish + fix publish condition for mapping
maxulysse Apr 27, 2022
f540226
fix output for seqkit
maxulysse Apr 27, 2022
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137 changes: 59 additions & 78 deletions conf/modules.config
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9 changes: 9 additions & 0 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -174,6 +174,12 @@
"samtools/bam2fq": {
"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
},
"samtools/bamtocram": {
"git_sha": "569e07f0af74e2a6ea43fca61ae90bb762893461"
},
"samtools/collatefastq": {
"git_sha": "705f8c9ac4dfdf07666e71abde28f267e2dfd5eb"
},
"samtools/faidx": {
"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
},
Expand Down Expand Up @@ -204,6 +210,9 @@
"strelka/somatic": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"tabix/bgzip": {
"git_sha": "37bf3936f3665483d070a5e0e0b314311032af7c"
},
"tabix/bgziptabix": {
"git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
},
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32 changes: 0 additions & 32 deletions modules/local/samtools/index/main.nf
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53 changes: 0 additions & 53 deletions modules/local/samtools/index/meta.yml
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31 changes: 0 additions & 31 deletions modules/local/samtools/mergecram/main.nf
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44 changes: 0 additions & 44 deletions modules/local/samtools/viewindex/meta.yml
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45 changes: 0 additions & 45 deletions modules/local/samtoolsview.nf
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12 changes: 5 additions & 7 deletions modules/local/samtools/viewindex/main.nf → ...f-core/modules/samtools/bamtocram/main.nf
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31 changes: 19 additions & 12 deletions modules/local/samtools/mergecram/meta.yml → ...-core/modules/samtools/bamtocram/meta.yml
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18 changes: 11 additions & 7 deletions modules/local/samtools/fastq/main.nf → ...ore/modules/samtools/collatefastq/main.nf
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