Merge pull request #26 from CenterForMedicalGeneticsGhent/dev

Dev

Author: matthdsm

.nf-core.yml

@@ -1,25 +1,27 @@
 repository_type: pipeline
 lint:
   files_exist:
-    - CODE_OF_CONDUCT.md
     - assets/nf-core-preprocessing_logo_light.png
+    - assets/nf-core-preprocessing_logo_dark.png
     - docs/images/nf-core-preprocessing_logo_light.png
     - docs/images/nf-core-preprocessing_logo_dark.png
-    - .github/ISSUE_TEMPLATE/config.yml
-    - .github/workflows/awstest.yml
-    - .github/workflows/awsfulltest.yml
+  files_unchanged:
+    - .github/CONTRIBUTING.md
+    - .github/ISSUE_TEMPLATE/feature_request.yml
     - .github/ISSUE_TEMPLATE/bug_report.yml
-    - conf/igenomes.config
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/workflows/branch.yml
+    - .github/workflows/linting.yml
+    - assets/email_template.html
+    - assets/email_template.txt
+    - assets/sendmail_template.txt
+    - docs/README.md
+    - lib/NfcoreTemplate.groovy
+    - .prettierignore
   nextflow_config:
     - manifest.name
     - manifest.homePage
-    - process.cpus
-    - process.memory
-    - process.time
-    - custom_config
   multiqc_config:
     - report_comment
-  files_unchanged:
-    - .github/ISSUE_TEMPLATE/bug_report.yml
   readme:
     - nextflow_badge

CHANGELOG.md

@@ -3,7 +3,15 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0dev - [date]
+## v1.1
+
+- Updated modules
+
+### `Fixed`
+
+- Bug with `fgbio/fastqtosam` where having multiple files per read requires a read structure
+
+## v1.0dev - [06/09/2022]
 
 Initial release of CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing, created with the [nf-core](https://nf-co.re/) template.
 

CITATIONS.md

@@ -15,9 +15,9 @@
 - [Biobambam2](https://gitlab.com/german.tischler/biobambam2)
   > Tischler, G., Leonard, S. biobambam: tools for read pair collation based algorithms on BAM files. Source Code Biol Med 9, 13 (2014). <https://doi.org/10.1186/1751-0473-9-13>
 - [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
-  > - Langmead B, Wilks C., Antonescu V., Charles R. Scaling read aligners to hundreds of threads on general-purpose processors. Bioinformatics.   bty648.
-  >- Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.
-  >- Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
+  > - Langmead B, Wilks C., Antonescu V., Charles R. Scaling read aligners to hundreds of threads on general-purpose processors. Bioinformatics. bty648.
+  > - Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.
+  > - Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
 - [BWA](http://bio-bwa.sourceforge.net/)
   > Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]
 - [FastP](https://github.com/OpenGene/fastp)
@@ -30,11 +30,11 @@
   > Picard Toolkit. 2019. Broad Institute, GitHub Repository. <https://broadinstitute.github.io/picard/>; Broad Institute
 - [Samtools](http://www.htslib.org/)
   > Twelve years of SAMtools and BCFtools
-Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li
-GigaScience, Volume 10, Issue 2, February 2021, giab008, <https://doi.org/10.1093/gigascience/giab008>
+  > Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li
+  > GigaScience, Volume 10, Issue 2, February 2021, giab008, <https://doi.org/10.1093/gigascience/giab008>
 - [Snap](http://snap.cs.berkeley.edu)
   > - Faster and More Accurate Sequence Alignment with SNAP. Matei Zaharia, William J. Bolosky, Kristal Curtis, Armando Fox, David Patterson, Scott Shenker, Ion Stoica, Richard M. Karp, and Taylor Sittler. arXiv:1111.5572v1, November 2011.
-  > - Fuzzy set intersection based paired-end short-read alignment.  William J. Bolosky, Arun Subramaniyan, Matei Zaharia, Ravi Pandya, Taylor Sittler, and David Patterson.  BioRxiv, November 2021.
+  > - Fuzzy set intersection based paired-end short-read alignment. William J. Bolosky, Arun Subramaniyan, Matei Zaharia, Ravi Pandya, Taylor Sittler, and David Patterson. BioRxiv, November 2021.
 
 ## Software packaging/containerisation tools
 

conf/cmgg.config

@@ -10,9 +10,6 @@ params {
     max_memory                  = 630.GB
     max_cpus                    = 75
     max_time                    = 72.h
-
-    hook_url                    = secrets.HOOK_URL
-
 }
 process {
     executor = 'slurm'

conf/modules.config

@@ -97,14 +97,20 @@ process {
     //********************************************************************************//
     // FASTQ CONVERSION
     //********************************************************************************//
+
+    withName: CAT_FASTQ {
+        publishDir = [ enabled: false ]
+    }
+
     withName: FGBIO_FASTQTOBAM {
         ext.args = {[
             "--read-group-id ${meta.readgroup.ID}",
             "--sample ${meta.readgroup.SM}",
             "--library ${meta.readgroup.LB}",
             "--platform-unit ${meta.readgroup.PU}",
             "--platform ${meta.readgroup.PL}",
-            "--sequencing-center ${meta.readgroup.CN}"
+            "--sequencing-center ${meta.readgroup.CN}",
+            "--sort=true"
         ].join(" ").trim()}
         publishDir = [ enabled: false ]
     }

modules.json

@@ -7,7 +7,7 @@
             "modules": {
                 "bclconvert": {
                     "branch": "master",
-                    "git_sha": "a9521de5ac03e1873c2746af2147600821fdaa49"
+                    "git_sha": "b98f1b77d1f6585995f00fb9189ad40c279417bd"
                 },
                 "biobambam/bamsormadup": {
                     "branch": "master",
@@ -21,29 +21,33 @@
                     "branch": "master",
                     "git_sha": "4f5274c3de0c9521f5033893ff61057a74c45ba9"
                 },
+                "cat/fastq": {
+                    "branch": "master",
+                    "git_sha": "c13f2274fb9c93ad265640e0e56e6526bd4f42d4"
+                },
                 "custom/dumpsoftwareversions": {
                     "branch": "master",
-                    "git_sha": "e5b44499efcf6f7fb24874886bac60591c5d94dd"
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "fastp": {
                     "branch": "master",
-                    "git_sha": "7e8ad566883449e7939062b5e2bcf53fc1e0002f"
+                    "git_sha": "2c70c1c1951aaf884d2e8d8d9c871db79f7b35aa"
                 },
                 "fgbio/fastqtobam": {
                     "branch": "master",
                     "git_sha": "36049bf544c2f3fad7508778b76f56c5e0fe1ee7"
                 },
                 "md5sum": {
                     "branch": "master",
-                    "git_sha": "bd1b80f36e1b9a978e598e4b47f6705ede34da37"
+                    "git_sha": "90aef30f432332bdf0ce9f4b9004aa5d5c4960bb"
                 },
                 "mosdepth": {
                     "branch": "master",
                     "git_sha": "72a31b76eb1b58879e0d91fb1d992e0118693098"
                 },
                 "multiqc": {
                     "branch": "master",
-                    "git_sha": "5138acca0985ca01c38a1c4fba917d83772b1106"
+                    "git_sha": "90aef30f432332bdf0ce9f4b9004aa5d5c4960bb"
                 },
                 "picard/collecthsmetrics": {
                     "branch": "master",
@@ -59,7 +63,7 @@
                 },
                 "samtools/convert": {
                     "branch": "master",
-                    "git_sha": "da79396f066a96450d9cc9f115c17c9d738595fd"
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "samtools/flagstat": {
                     "branch": "master",
@@ -79,7 +83,7 @@
                 },
                 "untar": {
                     "branch": "master",
-                    "git_sha": "51be617b1ca9bff973655eb899d591ed6ab253b5"
+                    "git_sha": "b63b9f752dc8e43fc70b0491aad5e0a270ab0e10"
                 }
             }
         }