moving config and primer files

configs/cecret_config_template.config

@@ -40,11 +40,11 @@
 //params.reads = 'reads'
 //params.single_reads = 'single_reads'
 //params.fastas = 'fastas'
-params.outdir = 'cecret'
+//params.outdir = 'cecret'
 
 //# Basic CPU usage grouping
-params.maxcpus = 8
-params.medcpus = 4
+//params.maxcpus = 8
+//params.medcpus = 4
 
 //# Specifying the 'sarscov2', 'mpx', or 'other'
 //params.species = 'sarscov2'
@@ -65,31 +65,6 @@ params.medcpus = 4
 //# muliple sequencing alignment options are 'mafft' or 'nextalign'
 //params.msa = 'mafft'
 
-//# Docker Images -------------------------------------------
-//# static containers (may become out of date)
-bcftools_container      = 'staphb/bcftools:1.16'
-bedtools_container      = 'staphb/bedtools:2.30.0'
-bwa_container           = 'staphb/bwa:0.7.17'
-fastp_container         = 'staphb/fastp:0.23.2'
-fastqc_container        = 'staphb/fastqc:0.11.9'
-freyja_container        = 'staphb/freyja:1.3.11'
-iqtree2_container       = 'staphb/iqtree2:2.1.2'
-ivar_container          = 'staphb/ivar:1.3.1'
-kraken2_container       = 'staphb/kraken2:2.1.2-no-db'
-mafft_container         = 'staphb/mafft:7.475'
-minimap2_container      = 'staphb/minimap2:2.24'
-multiqc_container       = 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0'
-pandas_container        = 'quay.io/biocontainers/pandas:1.1.5'
-samtools_container      = 'staphb/samtools:1.16'
-seqyclean_container     = 'staphb/seqyclean:1.10.09'
-snp_dists_container     = 'staphb/snp-dists:0.8.2'
-vadr_container          = 'staphb/vadr:1.5'
-
-//# latest tags (more likely to break workflow, but they update "too frequently")
-nextalign_container     = 'nextstrain/nextalign:latest'
-nextclade_container     = 'nextstrain/nextclade:latest'
-pangolin_container      = 'staphb/pangolin:latest'
-
 //# Workflow parameters --------------------------------------
 
 //# For process seqyclean
@@ -247,118 +222,119 @@ pangolin_container      = 'staphb/pangolin:latest'
 //params.multiqc = true
 //params.multiqc_options = ''
 
-process {
-  publishDir = [ path: params.outdir, mode: 'copy' ]
-
-  errorStrategy = 'retry'
-  maxRetries = 1
-
-  withLabel: maxcpus {
-    cpus = params.maxcpus
-  }
-  withLabel: medcpus {
-    cpus = params.medcpus
-  }
-
-  withName:download {
-    container = pandas_container
-  }
-
-  withName:fastqc{
-    container = fastqc_container
-  }
-
-  withName:seqyclean{
-    container = seqyclean_container
-  }
-
-  withName:fastp{
-    container = fastp_container
-  }
-
-  withName:bwa{
-    container = bwa_container
-    publishDir = [ path: "${params.outdir}", mode: 'copy', pattern: 'logs/*/*log' ]
-  }
-
-  withName:minimap2{
-    container = minimap2_container
-    publishDir = [ path: "${params.outdir}", mode: 'copy', pattern: 'logs/*/*log' ]
-  }
-
-  withName:'ivar_.*'{
-    container = ivar_container
-  }
-
-  withName:ivar_consensus{
-    memory = '8 GB'
-    container = ivar_container
-  }
-
-  withName:fasta_prep{
-    container = pandas_container
-  }
-
-  withName:bcftools_variants{
-   container = bcftools_container
-  }
-
-  withName:kraken2{
-    container = kraken2_container
-  }
-
-  withName:bedtools_multicov{
-    container = bedtools_container
-  }
-
-  withName:'samtools_.*'{
-    container = samtools_container
-  }
-
-  withName:pangolin{
-    container = pangolin_container
-  }
-
-  withName:'freyja.*'{
-    container = freyja_container
-  }
-
-  withName:nextclade{
-    container = nextclade_container
-  }
-
-  withName:vadr{
-    container = vadr_container
-    errorStrategy = 'ignore'
-  }
-
-  withName:summary{
-    container = pandas_container
-  }
-
-  withName:combine_results{
-    container = pandas_container
-  }
-
-  withName:mafft{
-    container = mafft_container
-    errorStrategy = 'retry'
-    maxRetries = 2
-  }
-
-  withName:nextalign{
-    container = nextalign_container
-  }
-
-  withName:snpdists{
-    container = snp_dists_container
-  }
-
-  withName:iqtree2{
-   container = iqtree2_container
-  }
-
-  withName:'multiqc.*'{
-   container = multiqc_container
-  }
-}
+//# ------------------------------------------------------------------------
+//# Examples of how to change containers or process directive values -------
+//# This is likely not current and should not be used as-is ----------------
+//# You've been warned <3 --------------------------------------------------
+
+//# Docker Images -------------------------------------------
+//# static containers (may become out of date)
+//bcftools_container      = 'staphb/bcftools:1.16'
+//bedtools_container      = 'staphb/bedtools:2.30.0'
+//bwa_container           = 'staphb/bwa:0.7.17'
+//fastp_container         = 'staphb/fastp:0.23.2'
+//fastqc_container        = 'staphb/fastqc:0.11.9'
+//freyja_container        = 'staphb/freyja:1.3.11'
+//iqtree2_container       = 'staphb/iqtree2:2.1.2'
+//ivar_container          = 'staphb/ivar:1.3.1'
+//kraken2_container       = 'staphb/kraken2:2.1.2-no-db'
+//mafft_container         = 'staphb/mafft:7.475'
+//minimap2_container      = 'staphb/minimap2:2.24'
+//multiqc_container       = 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0'
+//pandas_container        = 'quay.io/biocontainers/pandas:1.1.5'
+//samtools_container      = 'staphb/samtools:1.16'
+//seqyclean_container     = 'staphb/seqyclean:1.10.09'
+//snp_dists_container     = 'staphb/snp-dists:0.8.2'
+//vadr_container          = 'staphb/vadr:1.5'
+
+//# latest tags (more likely to break workflow, but they update "too frequently")
+//nextalign_container     = 'nextstrain/nextalign:latest'
+//nextclade_container     = 'nextstrain/nextclade:latest'
+//pangolin_container      = 'staphb/pangolin:latest'
+
+
+//# Changing the directives for processes
+//# The processes can be found in Grandeur/modules and their names are
+//bcftools_variants
+//bedtools_multicov
+//bwa
+//fasta_prep
+//summary
+//combine_results
+//download
+//fastp
+//fastqc
+//freyja
+//freyja_aggregate
+//iqtree2
+//ivar_consensus
+//ivar_variants
+//ivar_trim
+//kraken2
+//mafft
+//minimap2
+//multiqc_combine
+//nextalign
+//nextclade
+//pangolin
+//samtools_stats
+//samtools_coverage
+//samtools_flagstat
+//samtools_depth
+//samtools_ampliconstats
+//samtools_plot_ampliconstats
+//samtools_sort
+//samtools_filter
+//samtools_ampliconclip
+//samtools_markdup
+//seqyclean
+//snpdists
+//vadr
+
+//# Adjusting the directives for a process
+//process {
+//  publishDir = [ path: params.outdir, mode: 'copy' ]
+//
+//  errorStrategy = 'retry'
+//  maxRetries = 1
+//
+//  withLabel: maxcpus {
+//    cpus = params.maxcpus
+//  }
+//  withLabel: medcpus {
+//    cpus = params.medcpus
+//  }
+//
+//  withName:download {
+//    container = pandas_container
+//  }
+//
+//  withName:fastqc{
+//    container = fastqc_container
+//  }
+//
+//  withName:bwa{
+//    container = bwa_container
+//    publishDir = [ path: "${params.outdir}", mode: 'copy', pattern: 'logs/*/*log' ]
+//  }
+//
+//  withName:minimap2{
+//    container = minimap2_container
+//    publishDir = [ path: "${params.outdir}", mode: 'copy', pattern: 'logs/*/*log' ]
+//  }
+//
+//  withName:'ivar_.*'{
+//    container = ivar_container
+//  }
+//
+//  withName:vadr{
+//    container = vadr_container
+//    errorStrategy = 'ignore'
+//  }
+//
+//  withName:mafft{
+//    container = mafft_container
+//    errorStrategy = 'retry'
+//    maxRetries = 2
+//  }
+//}

configs/docker.config

@@ -1,6 +1,2 @@
-docker {
-  enabled = true
-  runOptions = "-u \$(id -u):\$(id -g)"
-}
-
-includeConfig 'cecret_config_template.config'
+docker.enabled = true
+docker.runOptions = "-u \$(id -u):\$(id -g)"

configs/singularity.config

@@ -1,4 +1,2 @@
 singularity.enabled = true
 singularity.autoMounts = true
-
-includeConfig 'cecret_config_template.config'

configs/test.config

@@ -0,0 +1,4 @@
+params.sra_accessions                  = ['SRR13957125', 'SRR13957170', 'SRR13957177' ]
+params.outdir                          = 'cecret_test'
+params.primer_set                      = 'ncov_V3'
+params.species                         = 'sarscov2'

configs/test1.config

@@ -0,0 +1,5 @@
+params.sra_accessions                  = ['SRR23040634']
+params.outdir                          = 'cecret_test1'
+params.primer_set                      = 'ncov_V4'
+params.cleaner                         = 'fastp'
+params.species                         = 'sarscov2'

configs/test2.config

@@ -0,0 +1,5 @@
+params.sra_accessions = ['SRR13957125', 'SRR13957170', 'SRR13957177' ]
+params.outdir         = 'cecret_test2'
+params.primer_set     = 'ncov_V3'
+params.species        = 'sarscov2'
+params.relatedness    = true

configs/uphl.config

@@ -0,0 +1,5 @@
+singularity.enabled    = true
+singularity.autoMounts = true
+singularity.cacheDir   = 'singularity'
+params.kraken2         = true
+params.kraken2_db      = '/Volumes/IDGenomics_NAS/Data/kraken2_db/h+v'