From 526a2221ac9677fcbc62a7612f93358deeb9ed48 Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Wed, 13 Nov 2024 16:05:44 -0800
Subject: [PATCH 01/13] chore: update dependencies

---
 modules.json                                  |  2 +-
 modules/local/align_bam/main.nf               |  6 +++---
 .../callandfilterduplexconsensusreads/main.nf |  6 +++---
 .../main.nf                                   |  6 +++---
 .../fgbio/callduplexconsensusreads/main.nf    |  6 +++---
 .../fgbio/callmolecularconsensusreads/main.nf |  6 +++---
 .../fgbio/collectduplexseqmetrics/main.nf     |  6 +++---
 modules/local/fgbio/fastqtobam/main.nf        |  6 +++---
 .../local/fgbio/filterconsensusreads/main.nf  |  6 +++---
 modules/local/fgbio/groupreadsbyumi/main.nf   |  6 +++---
 modules/nf-core/bwa/index/environment.yml     |  1 +
 modules/nf-core/fastqc/environment.yml        |  1 +
 modules/nf-core/fgbio/sortbam/environment.yml |  4 +++-
 modules/nf-core/fgbio/sortbam/main.nf         |  4 ++--
 .../fgbio/sortbam/tests/main.nf.test.snap     | 20 +++++++++----------
 modules/nf-core/multiqc/environment.yml       |  1 +
 modules/nf-core/samtools/dict/environment.yml |  3 +--
 .../nf-core/samtools/faidx/environment.yml    |  3 +--
 .../nf-core/samtools/merge/environment.yml    |  3 +--
 19 files changed, 49 insertions(+), 47 deletions(-)

diff --git a/modules.json b/modules.json
index 890a1bb..4398c84 100644
--- a/modules.json
+++ b/modules.json
@@ -17,7 +17,7 @@
                     },
                     "fgbio/sortbam": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "bc6d86f063cd2e15015a339769c9ed18e5185a74",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
diff --git a/modules/local/align_bam/main.nf b/modules/local/align_bam/main.nf
index f4cfb0f..3097e2a 100644
--- a/modules/local/align_bam/main.nf
+++ b/modules/local/align_bam/main.nf
@@ -2,10 +2,10 @@ process ALIGN_BAM {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::fgbio=2.0.2 bioconda::bwa=0.7.17 bioconda::samtools=1.16.1"
+    conda "bioconda::fgbio=2.4.0 bioconda::bwa=0.7.18 bioconda::samtools=1.21"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-69f5207f538e4de9ef3bae6f9a95c5af56a88ab8:82d3ec41f9f1227f7183d344be46f73365efa704-0' :
-        'quay.io/biocontainers/mulled-v2-69f5207f538e4de9ef3bae6f9a95c5af56a88ab8:82d3ec41f9f1227f7183d344be46f73365efa704-0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/22/22e054c20192395e0e143df6c36fbed6ce4bd404feba05793aff16819e01fff1/data' :
+        'community.wave.seqera.io/library/fgbio_bwa_samtools:6fad70472c85d4d3' }"
 
     input:
     tuple val(meta), path(unmapped_bam)
diff --git a/modules/local/fgbio/callandfilterduplexconsensusreads/main.nf b/modules/local/fgbio/callandfilterduplexconsensusreads/main.nf
index 32d9be1..40d1839 100644
--- a/modules/local/fgbio/callandfilterduplexconsensusreads/main.nf
+++ b/modules/local/fgbio/callandfilterduplexconsensusreads/main.nf
@@ -2,10 +2,10 @@ process FGBIO_CALLANDFILTERDUPLEXCONSENSUSREADS {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::fgbio=2.0.2"
+    conda "bioconda::fgbio=2.4.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
-        'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' :
+        'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }"
 
     input:
     tuple val(meta), path(grouped_bam)
diff --git a/modules/local/fgbio/callandfiltermolecularconsensusreads/main.nf b/modules/local/fgbio/callandfiltermolecularconsensusreads/main.nf
index 9fedadb..b4a5eea 100644
--- a/modules/local/fgbio/callandfiltermolecularconsensusreads/main.nf
+++ b/modules/local/fgbio/callandfiltermolecularconsensusreads/main.nf
@@ -2,10 +2,10 @@ process FGBIO_CALLANDFILTERMOLECULARCONSENSUSREADS {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::fgbio=2.0.2"
+    conda "bioconda::fgbio=2.4.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
-        'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' :
+        'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }"
 
     input:
     tuple val(meta), path(grouped_bam)
diff --git a/modules/local/fgbio/callduplexconsensusreads/main.nf b/modules/local/fgbio/callduplexconsensusreads/main.nf
index 939065d..864db45 100644
--- a/modules/local/fgbio/callduplexconsensusreads/main.nf
+++ b/modules/local/fgbio/callduplexconsensusreads/main.nf
@@ -2,10 +2,10 @@ process FGBIO_CALLDDUPLEXCONSENSUSREADS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::fgbio=2.0.2"
+    conda "bioconda::fgbio=2.4.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
-        'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' :
+        'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }"
 
     input:
     tuple val(meta), path(grouped_bam)
diff --git a/modules/local/fgbio/callmolecularconsensusreads/main.nf b/modules/local/fgbio/callmolecularconsensusreads/main.nf
index 6bf303d..e367a03 100644
--- a/modules/local/fgbio/callmolecularconsensusreads/main.nf
+++ b/modules/local/fgbio/callmolecularconsensusreads/main.nf
@@ -2,10 +2,10 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::fgbio=2.0.2"
+    conda "bioconda::fgbio=2.4.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
-        'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' :
+        'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }"
 
     input:
     tuple val(meta), path(grouped_bam)
diff --git a/modules/local/fgbio/collectduplexseqmetrics/main.nf b/modules/local/fgbio/collectduplexseqmetrics/main.nf
index 4675898..df3255b 100644
--- a/modules/local/fgbio/collectduplexseqmetrics/main.nf
+++ b/modules/local/fgbio/collectduplexseqmetrics/main.nf
@@ -2,10 +2,10 @@ process FGBIO_COLLECTDUPLEXSEQMETRICS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::fgbio=2.0.2"
+    conda "bioconda::fgbio=2.4.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
-        'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' :
+        'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }"
 
     input:
     tuple val(meta), path(grouped_bam)
diff --git a/modules/local/fgbio/fastqtobam/main.nf b/modules/local/fgbio/fastqtobam/main.nf
index 543b97f..2365cda 100644
--- a/modules/local/fgbio/fastqtobam/main.nf
+++ b/modules/local/fgbio/fastqtobam/main.nf
@@ -2,10 +2,10 @@ process FGBIO_FASTQTOBAM {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::fgbio=2.0.2"
+    conda "bioconda::fgbio=2.4.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
-        'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' :
+        'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }"
 
     input:
     tuple val(meta), path(fastqs)
diff --git a/modules/local/fgbio/filterconsensusreads/main.nf b/modules/local/fgbio/filterconsensusreads/main.nf
index 6943765..e7814a4 100644
--- a/modules/local/fgbio/filterconsensusreads/main.nf
+++ b/modules/local/fgbio/filterconsensusreads/main.nf
@@ -2,10 +2,10 @@ process FGBIO_FILTERCONSENSUSREADS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::fgbio=2.0.2 bioconda::samtools=1.16.1"
+    conda "bioconda::fgbio=2.4.0 bioconda::samtools=1.21"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-69f5207f538e4de9ef3bae6f9a95c5af56a88ab8:82d3ec41f9f1227f7183d344be46f73365efa704-0' :
-        'quay.io/biocontainers/mulled-v2-69f5207f538e4de9ef3bae6f9a95c5af56a88ab8:82d3ec41f9f1227f7183d344be46f73365efa704-0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/22/22e054c20192395e0e143df6c36fbed6ce4bd404feba05793aff16819e01fff1/data' :
+        'community.wave.seqera.io/library/fgbio_bwa_samtools:6fad70472c85d4d3' }"
 
     input:
     tuple val(meta), path(consensus_bam)
diff --git a/modules/local/fgbio/groupreadsbyumi/main.nf b/modules/local/fgbio/groupreadsbyumi/main.nf
index e650599..c710c69 100644
--- a/modules/local/fgbio/groupreadsbyumi/main.nf
+++ b/modules/local/fgbio/groupreadsbyumi/main.nf
@@ -2,10 +2,10 @@ process FGBIO_GROUPREADSBYUMI {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::fgbio=2.0.2"
+    conda "bioconda::fgbio=2.4.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
-        'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' :
+        'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }"
 
     input:
     tuple val(meta), path(mapped_bam)
diff --git a/modules/nf-core/bwa/index/environment.yml b/modules/nf-core/bwa/index/environment.yml
index d8789a2..694a387 100644
--- a/modules/nf-core/bwa/index/environment.yml
+++ b/modules/nf-core/bwa/index/environment.yml
@@ -1,3 +1,4 @@
+name: bwa_index
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
index 691d4c7..0d5be45 100644
--- a/modules/nf-core/fastqc/environment.yml
+++ b/modules/nf-core/fastqc/environment.yml
@@ -1,3 +1,4 @@
+name: fastqc
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/fgbio/sortbam/environment.yml b/modules/nf-core/fgbio/sortbam/environment.yml
index 6f3c756..18922f1 100644
--- a/modules/nf-core/fgbio/sortbam/environment.yml
+++ b/modules/nf-core/fgbio/sortbam/environment.yml
@@ -1,5 +1,7 @@
+name: fgbio_sortbam
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::fgbio=2.2.1
+  # renovate: datasource=conda depName=bioconda/fgbio
+  - bioconda::fgbio=2.4.0
diff --git a/modules/nf-core/fgbio/sortbam/main.nf b/modules/nf-core/fgbio/sortbam/main.nf
index e061f7c..818cdb4 100644
--- a/modules/nf-core/fgbio/sortbam/main.nf
+++ b/modules/nf-core/fgbio/sortbam/main.nf
@@ -4,8 +4,8 @@ process FGBIO_SORTBAM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fgbio:2.2.1--hdfd78af_0' :
-        'biocontainers/fgbio:2.2.1--hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' :
+        'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/fgbio/sortbam/tests/main.nf.test.snap b/modules/nf-core/fgbio/sortbam/tests/main.nf.test.snap
index 39761a9..6f437ba 100644
--- a/modules/nf-core/fgbio/sortbam/tests/main.nf.test.snap
+++ b/modules/nf-core/fgbio/sortbam/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,384c5398cae017e4fe0df8cb8f004017"
+                    "versions.yml:md5,2d127286141b26c7cf87e99f2875d10e"
                 ],
                 "bam": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,384c5398cae017e4fe0df8cb8f004017"
+                    "versions.yml:md5,2d127286141b26c7cf87e99f2875d10e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-21T05:37:31.605753331"
+        "timestamp": "2024-11-11T12:26:05.650691"
     },
     "sarscov2 - bam": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,384c5398cae017e4fe0df8cb8f004017"
+                    "versions.yml:md5,2d127286141b26c7cf87e99f2875d10e"
                 ],
                 "bam": [
                     [
@@ -55,14 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,384c5398cae017e4fe0df8cb8f004017"
+                    "versions.yml:md5,2d127286141b26c7cf87e99f2875d10e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-21T10:48:47.945706955"
+        "timestamp": "2024-11-11T12:25:53.613141"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 6f5b867..66bbefa 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -1,3 +1,4 @@
+name: multiqc
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/samtools/dict/environment.yml b/modules/nf-core/samtools/dict/environment.yml
index 62054fc..31d4545 100644
--- a/modules/nf-core/samtools/dict/environment.yml
+++ b/modules/nf-core/samtools/dict/environment.yml
@@ -1,5 +1,4 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: samtools_dict
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml
index 62054fc..887abf2 100644
--- a/modules/nf-core/samtools/faidx/environment.yml
+++ b/modules/nf-core/samtools/faidx/environment.yml
@@ -1,5 +1,4 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: samtools_faidx
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml
index 62054fc..e119a31 100644
--- a/modules/nf-core/samtools/merge/environment.yml
+++ b/modules/nf-core/samtools/merge/environment.yml
@@ -1,5 +1,4 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: samtools_merge
 channels:
   - conda-forge
   - bioconda

From f551cde01a47882f05c01825cee4c5eddfa7b311 Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Wed, 13 Nov 2024 16:09:43 -0800
Subject: [PATCH 02/13] chore: update changelog

---
 CHANGELOG.md | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b39a78a..300a024 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,8 +7,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [PR #90](https://github.com/nf-core/fastquorum/pull/90) - Update dependency versions in fastquorum environments
+  | Dependency | Previous Version | New Version |
+  | ---------- | ---------------- | ----------- |
+  | bwa | 0.7.17 | 0.7.18 |
+  | fgbio | 2.0.2 | 2.4.0 |
+  | samtools | 1.16.1 | 1.21 |
 - [PR #87](https://github.com/nf-core/fastquorum/pull/87) - Raise minimum version to 24.04.2
-- [PR #84](https://github.com/nf-core/fastquorum/pull/84) - Update to nf-core/tools template version 3.0.2
+- [PR #84](https://github.com/nf-core/fastquorum/pull/84) - Update to nf-core/tools template version 3.0.2 and update nf-core modules
+  | Module | Previous SHA | New SHA |
+  | -------- | ---------------- | ----------- |
+  | bwa/index | e0ff65e | 6666521 |
+  | fastqc | b49b899 | 6666521 |
+  | fgbio/sortbam | 2fc7438 | bc6d86f |
+  | multiqc | fe9614c | cf17ca4 |
+  | samtools/dict | 3c8fd07 | b13f07b |
+  | samtools/faidx | 04fbbc7 | b13f07b |
+  | samtools/merge | 04fbbc7 | b13f07b |
 - [PR #79](https://github.com/nf-core/fastquorum/pull/79) and [PR #80](https://github.com/nf-core/fastquorum/pull/90) - Publish aligned consensus bai file
 
 ### Credits

From ecd433a22b9fb9b9ad47ef239cff3b248076d6d6 Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Wed, 13 Nov 2024 16:10:37 -0800
Subject: [PATCH 03/13] chore: arrange changelog

---
 CHANGELOG.md | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 300a024..992f65b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,17 +13,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   | bwa | 0.7.17 | 0.7.18 |
   | fgbio | 2.0.2 | 2.4.0 |
   | samtools | 1.16.1 | 1.21 |
+
+  | Module         | Previous SHA | New SHA |
+  | -------------- | ------------ | ------- |
+  | bwa/index      | e0ff65e      | 6666521 |
+  | fastqc         | b49b899      | 6666521 |
+  | fgbio/sortbam  | 2fc7438      | bc6d86f |
+  | multiqc        | fe9614c      | cf17ca4 |
+  | samtools/dict  | 3c8fd07      | b13f07b |
+  | samtools/faidx | 04fbbc7      | b13f07b |
+  | samtools/merge | 04fbbc7      | b13f07b |
+
 - [PR #87](https://github.com/nf-core/fastquorum/pull/87) - Raise minimum version to 24.04.2
-- [PR #84](https://github.com/nf-core/fastquorum/pull/84) - Update to nf-core/tools template version 3.0.2 and update nf-core modules
-  | Module | Previous SHA | New SHA |
-  | -------- | ---------------- | ----------- |
-  | bwa/index | e0ff65e | 6666521 |
-  | fastqc | b49b899 | 6666521 |
-  | fgbio/sortbam | 2fc7438 | bc6d86f |
-  | multiqc | fe9614c | cf17ca4 |
-  | samtools/dict | 3c8fd07 | b13f07b |
-  | samtools/faidx | 04fbbc7 | b13f07b |
-  | samtools/merge | 04fbbc7 | b13f07b |
+- [PR #84](https://github.com/nf-core/fastquorum/pull/84) - Update to nf-core/tools template version 3.0.2
 - [PR #79](https://github.com/nf-core/fastquorum/pull/79) and [PR #80](https://github.com/nf-core/fastquorum/pull/90) - Publish aligned consensus bai file
 
 ### Credits

From d73116b9bfd05548f7f61f3eb5c6e9b964101f68 Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Thu, 14 Nov 2024 08:28:06 -0800
Subject: [PATCH 04/13] chore: update snaps

---
 tests/pipeline/multi_fastq.nf.test.snap  | 14 +++++------
 tests/pipeline/multi_lanes.nf.test.snap  |  8 +++----
 tests/pipeline/single_fastq.nf.test.snap | 30 ++++++++++++------------
 tests/pipeline/tiny.nf.test.snap         | 14 +++++------
 4 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/tests/pipeline/multi_fastq.nf.test.snap b/tests/pipeline/multi_fastq.nf.test.snap
index 982612c..597aa6e 100644
--- a/tests/pipeline/multi_fastq.nf.test.snap
+++ b/tests/pipeline/multi_fastq.nf.test.snap
@@ -16,23 +16,23 @@
     },
     "multi_fastq_ht_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-23T11:52:45.734188"
+        "timestamp": "2024-11-13T16:19:04.373227"
     },
     "multi_fastq_rd_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, FILTERCONSENSUSREADS={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-23T11:50:06.73123"
+        "timestamp": "2024-11-13T16:16:02.887442"
     },
     "multi_fastq_ht": {
         "content": [
@@ -49,4 +49,4 @@
         },
         "timestamp": "2024-05-20T01:58:10.241449"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/pipeline/multi_lanes.nf.test.snap b/tests/pipeline/multi_lanes.nf.test.snap
index 297a526..fb7bf5d 100644
--- a/tests/pipeline/multi_lanes.nf.test.snap
+++ b/tests/pipeline/multi_lanes.nf.test.snap
@@ -1,13 +1,13 @@
 {
     "multi_lanes_rd_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, MERGE_BAM={samtools=1.21}, SORTBAM={fgbio=2.2.1}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, FILTERCONSENSUSREADS={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, MERGE_BAM={samtools=1.21}, SORTBAM={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-31T14:39:27.884022"
+        "timestamp": "2024-11-13T16:23:06.347717"
     },
     "multi_lanes_ht": {
         "content": [
@@ -26,13 +26,13 @@
     },
     "multi_lanes_ht_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, MERGE_BAM={samtools=1.21}, SORTBAM={fgbio=2.2.1}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, MERGE_BAM={samtools=1.21}, SORTBAM={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-31T14:42:58.125095"
+        "timestamp": "2024-11-13T16:26:31.69708"
     },
     "multi_lanes_rd": {
         "content": [
diff --git a/tests/pipeline/single_fastq.nf.test.snap b/tests/pipeline/single_fastq.nf.test.snap
index 2d4eb90..1f46218 100644
--- a/tests/pipeline/single_fastq.nf.test.snap
+++ b/tests/pipeline/single_fastq.nf.test.snap
@@ -1,42 +1,42 @@
 {
     "single_fastq_rd": {
         "content": [
-            "SRR6109255_one_fastq.grouped-family-sizes.txt:md5,8ee886d2141217391ed659819c0f37c0"
+            "SRR6109255_one_fastq.grouped-family-sizes.txt:md5,29eb69ede70485d5893c581211586590"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-20T07:33:11.408542"
+        "timestamp": "2024-11-13T16:29:47.975703"
     },
     "single_fastq_ht_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERMOLECULARCONSENSUSREADS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLANDFILTERMOLECULARCONSENSUSREADS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-23T11:56:22.904524"
+        "timestamp": "2024-11-13T16:32:31.491983"
     },
     "single_fastq_rd_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLMOLECULARCONSENSUSREADS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLMOLECULARCONSENSUSREADS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, FILTERCONSENSUSREADS={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-23T11:54:37.217511"
+        "timestamp": "2024-11-13T16:29:47.970557"
     },
     "single_fastq_ht": {
         "content": [
-            "SRR6109255_one_fastq.grouped-family-sizes.txt:md5,8ee886d2141217391ed659819c0f37c0"
+            "SRR6109255_one_fastq.grouped-family-sizes.txt:md5,29eb69ede70485d5893c581211586590"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-20T07:39:38.166122"
+        "timestamp": "2024-11-13T16:32:31.496755"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/pipeline/tiny.nf.test.snap b/tests/pipeline/tiny.nf.test.snap
index d595bac..be670cf 100644
--- a/tests/pipeline/tiny.nf.test.snap
+++ b/tests/pipeline/tiny.nf.test.snap
@@ -1,23 +1,23 @@
 {
     "tiny_rd_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, FILTERCONSENSUSREADS={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-23T11:38:48.555493"
+        "timestamp": "2024-11-13T16:35:50.97039"
     },
     "tiny_ht_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-23T11:40:38.676264"
+        "timestamp": "2024-11-13T16:38:43.703611"
     },
     "tiny_rd": {
         "content": [
@@ -41,4 +41,4 @@
         },
         "timestamp": "2024-05-19T23:48:57.112733"
     }
-}
+}
\ No newline at end of file

From 5dab71fa26c1bad5905ad2af56e5d586afbbd636 Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Thu, 14 Nov 2024 10:53:05 -0800
Subject: [PATCH 05/13] fix: allow non-gzipped fastq files

---
 assets/schema_input.json | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 460716d..236ee75 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -17,15 +17,15 @@
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "pattern": "^\\S+\\.f(ast)?q(\\.gz)?$",
+                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq', '.fastq', '.fq.gz' or '.fastq.gz'"
             },
             "fastq_2": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "pattern": "^\\S+\\.f(ast)?q(\\.gz)?$",
+                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq', '.fastq', '.fq.gz' or '.fastq.gz'"
             },
             "fastq_3": {
                 "type": "string",

From fb6854de14f9e9dee09bd2b5314163c285c03c1b Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Thu, 14 Nov 2024 10:59:33 -0800
Subject: [PATCH 06/13] fix: allow non-gzipped fq 3 and 4

---
 assets/schema_input.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 236ee75..8613d0a 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -31,14 +31,14 @@
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "pattern": "^\\S+\\.f(ast)?q(\\.gz)?$",
                 "errorMessage": "FastQ file for reads 3 (e.g. index1/i7) cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "fastq_4": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "pattern": "^\\S+\\.f(ast)?q(\\.gz)?$",
                 "errorMessage": "FastQ file for reads 4 (e.g. index2/i5) cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "read_structure": {

From 728d14dd4491d68c76cecd68ba9c63a1570817d4 Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Thu, 14 Nov 2024 11:02:44 -0800
Subject: [PATCH 07/13] chore: update usage

---
 docs/usage.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index a057792..1806a7a 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -77,10 +77,10 @@ TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,12M+T +T
 | Column           | Description                                                                                                                                                                            |
 | ---------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `sample`         | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
-| `fastq_1`        | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
-| `fastq_2`        | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
-| `fastq_3`        | Full path to FastQ file for Illumina short reads 3 (e.g. index1/i7). File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                            |
-| `fastq_4`        | Full path to FastQ file for Illumina short reads 4 (e.g. index2/i5). File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                            |
+| `fastq_1`        | Full path to FastQ file for Illumina short reads 1. File has to have the extension ".fastq", ".fq", ".fastq.gz" or ".fq.gz".                                                           |
+| `fastq_2`        | Full path to FastQ file for Illumina short reads 2. File has to have the extension ".fastq", ".fq", ".fastq.gz" or ".fq.gz".                                                           |
+| `fastq_3`        | Full path to FastQ file for Illumina short reads 3 (e.g. index1/i7). File has to have the extension ".fastq", ".fq", ".fastq.gz" or ".fq.gz".                                          |
+| `fastq_4`        | Full path to FastQ file for Illumina short reads 4 (e.g. index2/i5). File has to have the extension ".fastq", ".fq", ".fastq.gz" or ".fq.gz".                                          |
 | `read_structure` | the [`read_structure`][read-structure-link] describes how the bases in a sequencing run should be allocated into logical reads, including the unique molecular index(es)               |
 
 [read-structure-link]: https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures

From 940d789392da81a95bd024a52c1cb9a9f730c66c Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Thu, 14 Nov 2024 11:05:56 -0800
Subject: [PATCH 08/13] chore: update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 992f65b..e0e5aa8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [PR #91](https://github.com/nf-core/fastquorum/pull/91) - Allow non-gzipped input fastq files
 - [PR #90](https://github.com/nf-core/fastquorum/pull/90) - Update dependency versions in fastquorum environments
   | Dependency | Previous Version | New Version |
   | ---------- | ---------------- | ----------- |

From 627a8497567474aeda6bade58322261102b99239 Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Thu, 14 Nov 2024 11:08:13 -0800
Subject: [PATCH 09/13] docs: update error messages

---
 assets/schema_input.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 8613d0a..19a142a 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -32,14 +32,14 @@
                 "format": "file-path",
                 "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q(\\.gz)?$",
-                "errorMessage": "FastQ file for reads 3 (e.g. index1/i7) cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "errorMessage": "FastQ file for reads 3 (e.g. index1/i7) cannot contain spaces and must have extension '.fq', '.fastq', '.fq.gz' or '.fastq.gz'"
             },
             "fastq_4": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q(\\.gz)?$",
-                "errorMessage": "FastQ file for reads 4 (e.g. index2/i5) cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "errorMessage": "FastQ file for reads 4 (e.g. index2/i5) cannot contain spaces and must have extension '.fq', '.fastq', '.fq.gz' or '.fastq.gz'"
             },
             "read_structure": {
                 "type": "string",

From c164e1f75111476d545a5ba21c777c035db382da Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Thu, 14 Nov 2024 11:09:30 -0800
Subject: [PATCH 10/13] chore: update PR number

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e0e5aa8..48fae78 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
-- [PR #91](https://github.com/nf-core/fastquorum/pull/91) - Allow non-gzipped input fastq files
+- [PR #93](https://github.com/nf-core/fastquorum/pull/93) - Allow non-gzipped input fastq files
 - [PR #90](https://github.com/nf-core/fastquorum/pull/90) - Update dependency versions in fastquorum environments
   | Dependency | Previous Version | New Version |
   | ---------- | ---------------- | ----------- |

From 4ab9baf03d70bd275c9a1418ebab62e9eaa51ff0 Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Fri, 15 Nov 2024 16:17:45 +0000
Subject: [PATCH 11/13] Add patch files

---
 modules.json                                  | 21 ++++++++++++-------
 modules/nf-core/bwa/index/bwa-index.diff      | 16 ++++++++++++++
 modules/nf-core/fastqc/fastqc.diff            | 16 ++++++++++++++
 .../nf-core/fgbio/sortbam/fgbio-sortbam.diff  | 16 ++++++++++++++
 modules/nf-core/multiqc/multiqc.diff          | 17 +++++++++++++++
 .../nf-core/samtools/dict/samtools-dict.diff  | 17 +++++++++++++++
 .../samtools/faidx/samtools-faidx.diff        | 20 ++++++++++++++++++
 .../samtools/merge/samtools-merge.diff        | 19 +++++++++++++++++
 8 files changed, 135 insertions(+), 7 deletions(-)
 create mode 100644 modules/nf-core/bwa/index/bwa-index.diff
 create mode 100644 modules/nf-core/fastqc/fastqc.diff
 create mode 100644 modules/nf-core/fgbio/sortbam/fgbio-sortbam.diff
 create mode 100644 modules/nf-core/multiqc/multiqc.diff
 create mode 100644 modules/nf-core/samtools/dict/samtools-dict.diff
 create mode 100644 modules/nf-core/samtools/faidx/samtools-faidx.diff
 create mode 100644 modules/nf-core/samtools/merge/samtools-merge.diff

diff --git a/modules.json b/modules.json
index 4398c84..1fc2158 100644
--- a/modules.json
+++ b/modules.json
@@ -8,37 +8,44 @@
                     "bwa/index": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/bwa/index/bwa-index.diff"
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/fastqc/fastqc.diff"
                     },
                     "fgbio/sortbam": {
                         "branch": "master",
                         "git_sha": "bc6d86f063cd2e15015a339769c9ed18e5185a74",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/fgbio/sortbam/fgbio-sortbam.diff"
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/multiqc/multiqc.diff"
                     },
                     "samtools/dict": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/samtools/dict/samtools-dict.diff"
                     },
                     "samtools/faidx": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/samtools/faidx/samtools-faidx.diff"
                     },
                     "samtools/merge": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/samtools/merge/samtools-merge.diff"
                     }
                 }
             },
diff --git a/modules/nf-core/bwa/index/bwa-index.diff b/modules/nf-core/bwa/index/bwa-index.diff
new file mode 100644
index 0000000..4865eb4
--- /dev/null
+++ b/modules/nf-core/bwa/index/bwa-index.diff
@@ -0,0 +1,16 @@
+Changes in module 'nf-core/bwa/index'
+'modules/nf-core/bwa/index/main.nf' is unchanged
+Changes in 'bwa/index/environment.yml':
+--- modules/nf-core/bwa/index/environment.yml
++++ modules/nf-core/bwa/index/environment.yml
+@@ -1,3 +1,4 @@
++name: bwa_index
+ channels:
+   - conda-forge
+   - bioconda
+
+'modules/nf-core/bwa/index/meta.yml' is unchanged
+'modules/nf-core/bwa/index/tests/main.nf.test' is unchanged
+'modules/nf-core/bwa/index/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/bwa/index/tests/tags.yml' is unchanged
+************************************************************
diff --git a/modules/nf-core/fastqc/fastqc.diff b/modules/nf-core/fastqc/fastqc.diff
new file mode 100644
index 0000000..6def7b0
--- /dev/null
+++ b/modules/nf-core/fastqc/fastqc.diff
@@ -0,0 +1,16 @@
+Changes in module 'nf-core/fastqc'
+'modules/nf-core/fastqc/main.nf' is unchanged
+Changes in 'fastqc/environment.yml':
+--- modules/nf-core/fastqc/environment.yml
++++ modules/nf-core/fastqc/environment.yml
+@@ -1,3 +1,4 @@
++name: fastqc
+ channels:
+   - conda-forge
+   - bioconda
+
+'modules/nf-core/fastqc/meta.yml' is unchanged
+'modules/nf-core/fastqc/tests/main.nf.test' is unchanged
+'modules/nf-core/fastqc/tests/tags.yml' is unchanged
+'modules/nf-core/fastqc/tests/main.nf.test.snap' is unchanged
+************************************************************
diff --git a/modules/nf-core/fgbio/sortbam/fgbio-sortbam.diff b/modules/nf-core/fgbio/sortbam/fgbio-sortbam.diff
new file mode 100644
index 0000000..1e6ce47
--- /dev/null
+++ b/modules/nf-core/fgbio/sortbam/fgbio-sortbam.diff
@@ -0,0 +1,16 @@
+Changes in module 'nf-core/fgbio/sortbam'
+Changes in 'fgbio/sortbam/environment.yml':
+--- modules/nf-core/fgbio/sortbam/environment.yml
++++ modules/nf-core/fgbio/sortbam/environment.yml
+@@ -1,3 +1,4 @@
++name: fgbio_sortbam
+ channels:
+   - conda-forge
+   - bioconda
+
+'modules/nf-core/fgbio/sortbam/main.nf' is unchanged
+'modules/nf-core/fgbio/sortbam/meta.yml' is unchanged
+'modules/nf-core/fgbio/sortbam/tests/main.nf.test' is unchanged
+'modules/nf-core/fgbio/sortbam/tests/tags.yml' is unchanged
+'modules/nf-core/fgbio/sortbam/tests/main.nf.test.snap' is unchanged
+************************************************************
diff --git a/modules/nf-core/multiqc/multiqc.diff b/modules/nf-core/multiqc/multiqc.diff
new file mode 100644
index 0000000..f8e8f14
--- /dev/null
+++ b/modules/nf-core/multiqc/multiqc.diff
@@ -0,0 +1,17 @@
+Changes in module 'nf-core/multiqc'
+Changes in 'multiqc/environment.yml':
+--- modules/nf-core/multiqc/environment.yml
++++ modules/nf-core/multiqc/environment.yml
+@@ -1,3 +1,4 @@
++name: multiqc
+ channels:
+   - conda-forge
+   - bioconda
+
+'modules/nf-core/multiqc/main.nf' is unchanged
+'modules/nf-core/multiqc/meta.yml' is unchanged
+'modules/nf-core/multiqc/tests/main.nf.test' is unchanged
+'modules/nf-core/multiqc/tests/nextflow.config' is unchanged
+'modules/nf-core/multiqc/tests/tags.yml' is unchanged
+'modules/nf-core/multiqc/tests/main.nf.test.snap' is unchanged
+************************************************************
diff --git a/modules/nf-core/samtools/dict/samtools-dict.diff b/modules/nf-core/samtools/dict/samtools-dict.diff
new file mode 100644
index 0000000..fcbc565
--- /dev/null
+++ b/modules/nf-core/samtools/dict/samtools-dict.diff
@@ -0,0 +1,17 @@
+Changes in module 'nf-core/samtools/dict'
+Changes in 'samtools/dict/environment.yml':
+--- modules/nf-core/samtools/dict/environment.yml
++++ modules/nf-core/samtools/dict/environment.yml
+@@ -1,5 +1,4 @@
+----
+-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
++name: samtools_dict
+ channels:
+   - conda-forge
+   - bioconda
+
+'modules/nf-core/samtools/dict/main.nf' is unchanged
+'modules/nf-core/samtools/dict/meta.yml' is unchanged
+'modules/nf-core/samtools/dict/tests/main.nf.test' is unchanged
+'modules/nf-core/samtools/dict/tests/main.nf.test.snap' is unchanged
+************************************************************
diff --git a/modules/nf-core/samtools/faidx/samtools-faidx.diff b/modules/nf-core/samtools/faidx/samtools-faidx.diff
new file mode 100644
index 0000000..1b0129e
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/samtools-faidx.diff
@@ -0,0 +1,20 @@
+Changes in module 'nf-core/samtools/faidx'
+Changes in 'samtools/faidx/environment.yml':
+--- modules/nf-core/samtools/faidx/environment.yml
++++ modules/nf-core/samtools/faidx/environment.yml
+@@ -1,5 +1,4 @@
+----
+-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
++name: samtools_faidx
+ channels:
+   - conda-forge
+   - bioconda
+
+'modules/nf-core/samtools/faidx/main.nf' is unchanged
+'modules/nf-core/samtools/faidx/meta.yml' is unchanged
+'modules/nf-core/samtools/faidx/tests/main.nf.test' is unchanged
+'modules/nf-core/samtools/faidx/tests/nextflow.config' is unchanged
+'modules/nf-core/samtools/faidx/tests/nextflow2.config' is unchanged
+'modules/nf-core/samtools/faidx/tests/tags.yml' is unchanged
+'modules/nf-core/samtools/faidx/tests/main.nf.test.snap' is unchanged
+************************************************************
diff --git a/modules/nf-core/samtools/merge/samtools-merge.diff b/modules/nf-core/samtools/merge/samtools-merge.diff
new file mode 100644
index 0000000..ef7c93b
--- /dev/null
+++ b/modules/nf-core/samtools/merge/samtools-merge.diff
@@ -0,0 +1,19 @@
+Changes in module 'nf-core/samtools/merge'
+Changes in 'samtools/merge/environment.yml':
+--- modules/nf-core/samtools/merge/environment.yml
++++ modules/nf-core/samtools/merge/environment.yml
+@@ -1,5 +1,4 @@
+----
+-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
++name: samtools_merge
+ channels:
+   - conda-forge
+   - bioconda
+
+'modules/nf-core/samtools/merge/main.nf' is unchanged
+'modules/nf-core/samtools/merge/meta.yml' is unchanged
+'modules/nf-core/samtools/merge/tests/index.config' is unchanged
+'modules/nf-core/samtools/merge/tests/main.nf.test' is unchanged
+'modules/nf-core/samtools/merge/tests/tags.yml' is unchanged
+'modules/nf-core/samtools/merge/tests/main.nf.test.snap' is unchanged
+************************************************************

From ef03b06a78f490685aae703168b4bd1ad35456b8 Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Fri, 15 Nov 2024 09:31:12 -0800
Subject: [PATCH 12/13] fix: remove offending diff line

---
 modules/nf-core/samtools/dict/samtools-dict.diff   | 1 -
 modules/nf-core/samtools/faidx/samtools-faidx.diff | 1 -
 modules/nf-core/samtools/merge/samtools-merge.diff | 1 -
 3 files changed, 3 deletions(-)

diff --git a/modules/nf-core/samtools/dict/samtools-dict.diff b/modules/nf-core/samtools/dict/samtools-dict.diff
index fcbc565..19af3a4 100644
--- a/modules/nf-core/samtools/dict/samtools-dict.diff
+++ b/modules/nf-core/samtools/dict/samtools-dict.diff
@@ -3,7 +3,6 @@ Changes in 'samtools/dict/environment.yml':
 --- modules/nf-core/samtools/dict/environment.yml
 +++ modules/nf-core/samtools/dict/environment.yml
 @@ -1,5 +1,4 @@
-----
 -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 +name: samtools_dict
  channels:
diff --git a/modules/nf-core/samtools/faidx/samtools-faidx.diff b/modules/nf-core/samtools/faidx/samtools-faidx.diff
index 1b0129e..bdb1fc2 100644
--- a/modules/nf-core/samtools/faidx/samtools-faidx.diff
+++ b/modules/nf-core/samtools/faidx/samtools-faidx.diff
@@ -3,7 +3,6 @@ Changes in 'samtools/faidx/environment.yml':
 --- modules/nf-core/samtools/faidx/environment.yml
 +++ modules/nf-core/samtools/faidx/environment.yml
 @@ -1,5 +1,4 @@
-----
 -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 +name: samtools_faidx
  channels:
diff --git a/modules/nf-core/samtools/merge/samtools-merge.diff b/modules/nf-core/samtools/merge/samtools-merge.diff
index ef7c93b..3f24163 100644
--- a/modules/nf-core/samtools/merge/samtools-merge.diff
+++ b/modules/nf-core/samtools/merge/samtools-merge.diff
@@ -3,7 +3,6 @@ Changes in 'samtools/merge/environment.yml':
 --- modules/nf-core/samtools/merge/environment.yml
 +++ modules/nf-core/samtools/merge/environment.yml
 @@ -1,5 +1,4 @@
-----
 -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 +name: samtools_merge
  channels:

From 9e604d858680b5772a0314dfb440069e18cf5b66 Mon Sep 17 00:00:00 2001
From: znorgaard <zach@fulcrumgenomics.com>
Date: Fri, 15 Nov 2024 09:33:53 -0800
Subject: [PATCH 13/13] chore: set release date

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 48fae78..2c59369 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 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).
 
-## [[1.0.2]](https://github.com/nf-core/fastquorum/releases/tag/1.0.2) -- 2024-11-06
+## [[1.0.2]](https://github.com/nf-core/fastquorum/releases/tag/1.0.2) -- 2024-11-15
 
 ### Enhancements & fixes