Merge pull request #685 from asp8200/update_nf_core_modules

Updating nf-core-modules
nf-core · Jul 28, 2022 · 89d1574 · 89d1574
2 parents a40a304 + 9118d64
commit 89d1574
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Showing 15 changed files with 40 additions and 17 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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 nf-core modules used by Sarek.
 - [#691](https://github.com/nf-core/sarek/pull/691) - To run the same pytest as before locally, use `PROFILE=docker`
 
 ### Fixed

diff --git a/modules.json b/modules.json
@@ -10,7 +10,7 @@
                 "git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
             },
             "bcftools/stats": {
-                "git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
+                "git_sha": "535975eb81c9e48eb0403c136b7f1dd7acb1afad"
             },
             "bwa/index": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
@@ -70,7 +70,7 @@
                 "git_sha": "973151e9eab9bac400aa99f099075a10cdd8e84c"
             },
             "fastp": {
-                "git_sha": "9b51362a532a14665f513cf987531f9ea5046b74"
+                "git_sha": "7e8ad566883449e7939062b5e2bcf53fc1e0002f"
             },
             "fastqc": {
                 "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
@@ -202,7 +202,7 @@
                 "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
             },
             "samtools/merge": {
-                "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
+                "git_sha": "720027275ccdc1363bb2a19c6412da148e31d94b"
             },
             "samtools/mpileup": {
                 "git_sha": "24e05f6097a5dde57dd80d33295ed120f1b81aef"

diff --git a/modules/nf-core/modules/bcftools/stats/main.nf b/modules/nf-core/modules/bcftools/stats/main.nf
diff --git a/modules/nf-core/modules/bcftools/stats/meta.yml b/modules/nf-core/modules/bcftools/stats/meta.yml
diff --git a/modules/nf-core/modules/fastp/main.nf b/modules/nf-core/modules/fastp/main.nf
diff --git a/modules/nf-core/modules/fastp/meta.yml b/modules/nf-core/modules/fastp/meta.yml
diff --git a/modules/nf-core/modules/samtools/merge/main.nf b/modules/nf-core/modules/samtools/merge/main.nf
diff --git a/modules/nf-core/modules/samtools/merge/meta.yml b/modules/nf-core/modules/samtools/merge/meta.yml
diff --git a/subworkflows/nf-core/alignment_to_fastq.nf b/subworkflows/nf-core/alignment_to_fastq.nf
diff --git a/subworkflows/nf-core/gatk4/recalibrate/main.nf b/subworkflows/nf-core/gatk4/recalibrate/main.nf
diff --git a/subworkflows/nf-core/gatk4/recalibrate_spark/main.nf b/subworkflows/nf-core/gatk4/recalibrate_spark/main.nf
diff --git a/subworkflows/nf-core/merge_index_bam.nf b/subworkflows/nf-core/merge_index_bam.nf
diff --git a/subworkflows/nf-core/merge_index_cram.nf b/subworkflows/nf-core/merge_index_cram.nf
diff --git a/subworkflows/nf-core/vcf_qc.nf b/subworkflows/nf-core/vcf_qc.nf
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
@@ -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)
@@ -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