Remove gfflu/snpeff processes from PR#29 for #35 bugfix

CHANGELOG.md

@@ -3,6 +3,12 @@
 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).
 
+## [[3.3.1](https://github.com/CFIA-NCFAD/nf-flu/releases/tag/3.3.1)] - 2023-08-02
+
+### Fixes
+
+* Conda/Mamba env creation when using `conda`/`mamba` profile (#35)
+
 ## [[3.3.0](https://github.com/CFIA-NCFAD/nf-flu/releases/tag/3.3.0)] - 2023-07-11
 
 This release migrates to more recently updated Influenza virus sequences since the last update for the [NCBI Influenza DB FTP data](https://ftp.ncbi.nih.gov/genomes/INFLUENZA/) was in 2020-10-13. By default, all Orthomyxoviridae virus sequences were parsed from the daily updated NCBI Viruses [`AllNucleotide.fa`](https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/AllNucleotide/) and [`AllNuclMetadata.csv.gz`](https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/AllNuclMetadata/AllNuclMetadata.csv.gz) and uploaded to [Figshare](https://figshare.com/articles/dataset/2023-06-14_-_NCBI_Viruses_-_Orthomyxoviridae/23608782) as Zstd compressed files. nf-flu no longer uses the [influenza.fna.gz](https://ftp.ncbi.nih.gov/genomes/INFLUENZA/influenza.fna.gz) and [genomeset.dat.gz](https://ftp.ncbi.nih.gov/genomes/INFLUENZA/genomeset.dat.gz) files for Influenza sequences and metadata, respectively.

assets/multiqc_config.yaml

@@ -34,12 +34,6 @@ module_order:
  info: 'This section of the report shows Bcftools calculated statistics after variant calling using Clair3/Medaka and filter frameshift'
  path_filters:
  - './bcftools/*'
- - snpeff:
- name: 'SnpEff'
- anchor: 'snpeff'
- info: SnpEff variant effect analysis results summary
- path_filters:
- - './snpeff/*'
 
 extra_fn_clean_exts:
  - type: remove
@@ -65,7 +59,6 @@ run_modules:
  - samtools
  - mosdepth
  - bcftools
- - snpeff
 
 sp:
  mosdepth/global_dist:

modules/local/multiqc.nf

@@ -13,7 +13,6 @@ process MULTIQC {
  path('samtools/*')
  path('mosdepth/*')
  path('bcftools/*')
- path('snpeff/*')
  path('software_versions/*')
  path(workflow_summary)
 

workflows/nanopore.nf

@@ -23,9 +23,6 @@ include { ZSTD_DECOMPRESS as ZSTD_DECOMPRESS_FASTA; ZSTD_DECOMPRESS as ZSTD_DECO
 include { CAT_DB } from '../modules/local/misc'
 include { CAT_CONSENSUS } from '../modules/local/misc'
 include { SEQTK_SEQ } from '../modules/local/seqtk_seq'
-include { GFFLU } from '../modules/local/gfflu'
-include { SNPEFF_BUILD } from '../modules/local/snpeff_build'
-include { SNPEFF_ANN } from '../modules/local/snpeff_ann'
 include { CHECK_SAMPLE_SHEET } from '../modules/local/check_sample_sheet'
 include { CHECK_REF_FASTA } from '../modules/local/check_ref_fasta'
 // using modified BLAST_MAKEBLASTDB from nf-core/modules to only move/publish BLAST DB files
@@ -215,25 +212,6 @@ workflow NANOPORE {
  ch_vcf_filter = BCF_FILTER_MEDAKA.out.vcf
  }
 
- ch_refseqs = SEQTK_SEQ.out.sample_info.map { [it[2], it[3]] }
- GFFLU(ch_refseqs)
-
- SNPEFF_BUILD(GFFLU.out.gff)
- ch_snpeff_ann_input = SEQTK_SEQ.out.sample_info
- .map { sample, segment, ref_id, fasta, reads ->
- return [ref_id, fasta, sample, segment]
- }
- .combine(SNPEFF_BUILD.out.db, by: 0) // seqid, ref_fasta, sample, segment, db, config
- .map { ref_id, fasta, sample, segment, _, db, config ->
- return [sample, segment, ref_id, fasta, db, config]
- }
- .combine(ch_vcf_filter, by: [0, 1, 2]) // sample, segment, ref_id, ref_fasta, vcf
- .map { sample, segment, ref_id, fasta, db, config, _, vcf ->
- return [sample, segment, vcf, ref_id, fasta, db, config]
- }
-
- SNPEFF_ANN(ch_snpeff_ann_input)
-
  VCF_FILTER_FRAMESHIFT(ch_vcf_filter)
  ch_versions = ch_versions.mix(VCF_FILTER_FRAMESHIFT.out.versions)
 
@@ -291,7 +269,6 @@ workflow NANOPORE {
  MINIMAP2.out.stats.collect().ifEmpty([]),
  MOSDEPTH_GENOME.out.mqc.collect().ifEmpty([]),
  BCFTOOLS_STATS.out.stats.collect().ifEmpty([]),
- SNPEFF_ANN.out.csv.collect{it[4]}.ifEmpty([]),
  SOFTWARE_VERSIONS.out.mqc_yml.collect(),
  ch_workflow_summary.collectFile(name: "workflow_summary_mqc.yaml")
  )