Added module stubs to enable merquryfk in stub test

Plant-Food-Research-Open · May 18, 2024 · 56777e0 · 56777e0
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Showing 31 changed files with 3,747 additions and 36 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,18 +11,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 2. Removed release-announcements GitHub workflow
 3. Added a list of nf-core contributors
 4. Added a launcher script for local testing `local_assemblyqc`
-5. Added a custom `BUNDLELINKS` module which respects direction when bundling `dnadiff` links [#82](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/82)
+5. Added a custom `BUNDLELINKS` module which respects direction when bundling `DNADIFF` links [#82](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/82)
 6. Added the ability to create linear synteny plot in addition to the circos plot [#74](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/74)
-7. Updated modules and sub-workflows: `bwa/index`, `bwa/mem`, `cat/cat`, `custom/checkgff3fastacorrespondence`, `custom/restoregffids`, `custom/shortenfastaids`, `gt/gff3`, `gt/gff3validator`, `gt/stat`, `ltrfinder`, `ltrharvest`, `ltrretriever/lai`, `ltrretriever/ltrretriever`, `samblaster`, `fasta_ltrretriever_lai`, `fastq_bwa_mem_samblaster`, `gff3_validate`, `custom/sratoolsncbisettings`, `fastp`, `fastqc`, `untar`, `seqkit/seq`, `seqkit/sort`, `fasta_explore_search_plot_tidk`
+7. Updated modules and sub-workflows: `BWA/INDEX`, `BWA/MEM`, `CAT/CAT`, `CUSTOM/CHECKGFF3FASTACORRESPONDENCE`, `CUSTOM/RESTOREGFFIDS`, `CUSTOM/SHORTENFASTAIDS`, `GT/GFF3`, `GT/GFF3VALIDATOR`, `GT/STAT`, `LTRFINDER`, `LTRHARVEST`, `LTRRETRIEVER/LAI`, `LTRRETRIEVER/LTRRETRIEVER`, `SAMBLASTER`, `FASTA_LTRRETRIEVER_LAI`, `FASTQ_BWA_MEM_SAMBLASTER`, `GFF3_VALIDATE`, `CUSTOM/SRATOOLSNCBISETTINGS`, `FASTP`, `FASTQC`, `UNTAR`, `SEQKIT/SEQ`, `SEQKIT/SORT`, `FASTA_EXPLORE_SEARCH_PLOT_TIDK`
 8. Locally bumped `bwa/index` version to `biocontainers/bwa:0.7.18--he4a0461_0`
 9. Now the `contamination_stops_pipeline` flag allows the pipeline to continue if contamination is detected. It's default value is `true` [#54](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/54)
-10. Updated `fcs-adaptor` to 0.5.0 which includes additional adaptors for PacBio and Nanopore technologies [#55](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/55)
-11. Now fasta ids are sorted in natural order for the HiC module [#76](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/76)
-12. Now using `FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS` for SRA downloads
-13. Added `MERQURYFK` module [#85](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/85)
-14. Replaced `GFF3_VALIDATE` sub-workflow with `GFF3_GT_GFF3_GFF3VALIDATOR_STAT`
-15. Replaced local `BUSCO` module with `FASTA_GXF_BUSCO_PLOT` sub-workflow [#75](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/75)
-16. Replaced local `NCBI_FCS_ADAPTOR` with nf-core module
+10. Now fasta ids are sorted in natural order for the HiC module [#76](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/76)
+11. Now using `FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS` for SRA downloads
+12. Added `MERQURYFK` module [#85](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/85)
+13. Replaced `GFF3_VALIDATE` sub-workflow with `GFF3_GT_GFF3_GFF3VALIDATOR_STAT`
+14. Replaced local `BUSCO` module with `FASTA_GXF_BUSCO_PLOT` sub-workflow [#75](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/75)
+15. Replaced local `NCBI_FCS_ADAPTOR` with nf-core module and updated to 0.5.0 which includes additional adaptors for PacBio and Nanopore technologies [#55](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/55)
+16. Locally added stubs for `FASTK/FASTK`, `MERQURYFK/MERQURYFK`, `SRATOOLS/FASTERQDUMP` and `SRATOOLS/PREFETCH`
 
 ### `Fixed`
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -245,10 +245,6 @@ process {
         ]
     }
 
-    withName: '.*:DOWNLOAD_HIC:SRATOOLS_FASTERQDUMP' {
-        ext.prefix = { "${meta.id}.sra.fastq" }
-    }
-
     withName: FASTQC_RAW {
         publishDir = [
             path: { "${params.outdir}/hic/fastqc_raw" },
@@ -332,10 +328,6 @@ process {
         ext.prefix = { "${meta.id}.fasta" }
     }
 
-    withName: '.*:DOWNLOAD_READS:SRATOOLS_FASTERQDUMP' {
-        ext.prefix = { "${meta.id}.sra.fastq" }
-    }
-
     withName: FASTK_FASTK {
         ext.args = "-k$params.merqury_kmer_length -t1"
     }

diff --git a/modules.json b/modules.json
@@ -133,7 +133,8 @@
                     "fastk/fastk": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/fastk/fastk/fastk-fastk.diff"
                     },
                     "fastp": {
                         "branch": "master",
@@ -158,7 +159,8 @@
                     "merquryfk/merquryfk": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff"
                     },
                     "seqkit/seq": {
                         "branch": "master",
@@ -173,12 +175,14 @@
                     "sratools/fasterqdump": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools", "modules"]
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools", "modules"],
+                        "patch": "modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff"
                     },
                     "sratools/prefetch": {
                         "branch": "master",
                         "git_sha": "1fc29f92e439d5631fdf34b8ac4687297d70f5ec",
-                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools", "modules"]
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools", "modules"],
+                        "patch": "modules/nf-core/sratools/prefetch/sratools-prefetch.diff"
                     },
                     "tidk/explore": {
                         "branch": "master",

diff --git a/modules/nf-core/fastk/fastk/environment.yml b/modules/nf-core/fastk/fastk/environment.yml