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Updating nf-core-modules #685

Merged
merged 8 commits into from
Jul 28, 2022
Merged

Updating nf-core-modules #685

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aae626c
Updating nf-core-modules
asp8200 Jul 25, 2022
4000df2
Updating changelog
asp8200 Jul 25, 2022
c1988be
Adding missing second parameter target_bed in call to BCFTOOLS_STATS
asp8200 Jul 25, 2022
cab4478
Merge branch 'dev' into update_nf_core_modules
asp8200 Jul 27, 2022
c7eaa65
WIP: Getting CI-tests working after updates of nf-core-modules
asp8200 Jul 27, 2022
b970314
Correcting call to MERGE_BAM
asp8200 Jul 27, 2022
89fcdf6
Fixing call to MERGE_INDEX_CRAM
asp8200 Jul 27, 2022
9118d64
Update CHANGELOG.md
asp8200 Jul 28, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Changed

- [#679](https://github.com/nf-core/sarek/pull/679) - Back to `dev`
- [#685](https://github.com/nf-core/sarek/pull/685) - Updating the
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- [#691](https://github.com/nf-core/sarek/pull/691) - To run the same pytest as before locally, use `PROFILE=docker`

### Fixed
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6 changes: 3 additions & 3 deletions modules.json
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Expand Up @@ -10,7 +10,7 @@
"git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
},
"bcftools/stats": {
"git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
"git_sha": "535975eb81c9e48eb0403c136b7f1dd7acb1afad"
},
"bwa/index": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
Expand Down Expand Up @@ -70,7 +70,7 @@
"git_sha": "973151e9eab9bac400aa99f099075a10cdd8e84c"
},
"fastp": {
"git_sha": "9b51362a532a14665f513cf987531f9ea5046b74"
"git_sha": "7e8ad566883449e7939062b5e2bcf53fc1e0002f"
},
"fastqc": {
"git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
Expand Down Expand Up @@ -202,7 +202,7 @@
"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
},
"samtools/merge": {
"git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
"git_sha": "720027275ccdc1363bb2a19c6412da148e31d94b"
},
"samtools/mpileup": {
"git_sha": "24e05f6097a5dde57dd80d33295ed120f1b81aef"
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8 changes: 7 additions & 1 deletion modules/nf-core/modules/bcftools/stats/main.nf
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5 changes: 5 additions & 0 deletions modules/nf-core/modules/bcftools/stats/meta.yml
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10 changes: 7 additions & 3 deletions modules/nf-core/modules/fastp/main.nf
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2 changes: 1 addition & 1 deletion modules/nf-core/modules/fastp/meta.yml
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3 changes: 2 additions & 1 deletion modules/nf-core/modules/samtools/merge/main.nf
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4 changes: 4 additions & 0 deletions modules/nf-core/modules/samtools/merge/meta.yml
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3 changes: 2 additions & 1 deletion subworkflows/nf-core/alignment_to_fastq.nf
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2 changes: 1 addition & 1 deletion subworkflows/nf-core/gatk4/recalibrate/main.nf
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2 changes: 1 addition & 1 deletion subworkflows/nf-core/gatk4/recalibrate_spark/main.nf
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2 changes: 1 addition & 1 deletion subworkflows/nf-core/merge_index_bam.nf
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3 changes: 2 additions & 1 deletion subworkflows/nf-core/merge_index_cram.nf
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2 changes: 1 addition & 1 deletion subworkflows/nf-core/vcf_qc.nf
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4 changes: 2 additions & 2 deletions workflows/sarek.nf
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Expand Up @@ -385,7 +385,7 @@ workflow SAREK {

// convert any bam input to fastq
// Fasta are not needed when converting bam to fastq -> []
ALIGNMENT_TO_FASTQ_INPUT(ch_input_sample_type.bam, [])
ALIGNMENT_TO_FASTQ_INPUT(ch_input_sample_type.bam, [], [])

// gather fastq (inputed or converted)
// Theorically this could work on mixed input (fastq for one sample and bam for another)
Expand Down Expand Up @@ -419,7 +419,7 @@ workflow SAREK {
bamtofastq = CREATE_UMI_CONSENSUS.out.consensusbam.map{meta, bam -> [meta,bam,[]]}

// convert back to fastq for further preprocessing
ALIGNMENT_TO_FASTQ_UMI(bamtofastq, [])
ALIGNMENT_TO_FASTQ_UMI(bamtofastq, [], [])

ch_reads_fastp = ALIGNMENT_TO_FASTQ_UMI.out.reads

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