Merge pull request #90 from nf-core/zn_conda

fix: conda environments

CHANGELOG.md

@@ -3,10 +3,28 @@
 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
 
+- [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 |
+  | ---------- | ---------------- | ----------- |
+  | 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
 - [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

assets/schema_input.json

@@ -17,29 +17,29 @@
                 "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",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 3 (e.g. index1/i7) cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "pattern": "^\\S+\\.f(ast)?q(\\.gz)?$",
+                "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$",
-                "errorMessage": "FastQ file for reads 4 (e.g. index2/i5) cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "pattern": "^\\S+\\.f(ast)?q(\\.gz)?$",
+                "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",

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

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": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "git_sha": "bc6d86f063cd2e15015a339769c9ed18e5185a74",
+                        "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"
                     }
                 }
             },

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)

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)

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)

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)

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)

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)

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)

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)

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)