Merge pull request #77 from CDCgov/dev

Release 1.4
CDCgov · Jun 27, 2022 · cc0fc6c · cc0fc6c
2 parents f8505d4 + b4bd506
commit cc0fc6c
Show file tree

Hide file tree

Showing 8 changed files with 40 additions and 15 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -15,7 +15,7 @@ process {
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
 
     errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
-    maxRetries    = 1
+    maxRetries    = 3
     maxErrors     = '-1'
 
     // Process-specific resource requirements
@@ -30,13 +30,13 @@ process {
         time   = { check_max( 72.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 4     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
+        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 16.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 72.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_high {
-        cpus   = { check_max( 4    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
+        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
+        memory = { check_max( 32.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 72.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_long {

diff --git a/conf/modules.config b/conf/modules.config
@@ -464,7 +464,7 @@ process {
     withName: 'SEQKIT_REPLACE' {
         ext.args            = { "-s -p '\\*' -r '-'" }
         ext.suffix          = { "fasta" }
-        ext.errorStrategy   = { "ignore" }
+        ext.errorStrategy   = { "retry" }
         ext.prefix          = { "vcf-to-fasta" }
         ext.when            = {  }
         publishDir          = [
@@ -476,7 +476,7 @@ process {
     }
     withName: 'SNPDISTS' {
         ext.args            = { "" }
-        ext.errorStrategy   = { "ignore" }
+        ext.errorStrategy   = { "retry" }
         ext.when            = {  }
         publishDir          = [
             enabled: true,

diff --git a/modules/local/downsample_rate.nf b/modules/local/downsample_rate.nf
@@ -1,15 +1,20 @@
 process DOWNSAMPLE_RATE {
     tag "$meta.id"
     label 'process_low'
-
+
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
+        'quay.io/biocontainers/python:3.8.3' }"
+
     input:
-    tuple val(meta), path(reads)
-	path(reference_fasta)
-	val(coverage)
-	val(rate)
+        tuple val(meta), path(reads)
+        path(reference_fasta)
+        val(coverage)
+        val(rate)
 
     output:
-    tuple val(meta), env(SAMPLE_RATE),  env(SAMPLED_NUM_READS),   emit: downsampled_rate
+        tuple val(meta), env(SAMPLE_RATE),  env(SAMPLED_NUM_READS),   emit: downsampled_rate
 	env(SAMPLED_NUM_READS)                                    ,   emit: number_to_sample
 
 	script:

diff --git a/modules/local/lane_merge.nf b/modules/local/lane_merge.nf
@@ -2,6 +2,11 @@ process LANE_MERGE {
 
     tag "$meta.id"
 
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
+        'quay.io/biocontainers/python:3.8.3' }"
+
     input:
     tuple val(meta), path(reads)
 

diff --git a/modules/local/qc_reportsheet.nf b/modules/local/qc_reportsheet.nf
@@ -1,6 +1,11 @@
 process QC_REPORTSHEET {
     label 'process_low'
 
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
+        'quay.io/biocontainers/python:3.8.3' }"
+
     input:
     path(qc_lines)
 
@@ -13,4 +18,4 @@ process QC_REPORTSHEET {
     sort ${qc_lines} > sorted.txt
     cat sorted.txt >> qc_report.txt
     """
-}
+}
diff --git a/modules/local/vcfqc.nf b/modules/local/vcfqc.nf
@@ -2,6 +2,11 @@ process VCF_QC {
     tag "vcf-qc"
     label 'process_low'
 
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
+        'quay.io/biocontainers/python:3.8.3' }"
+
     input:
     path(vcffasta)
 

diff --git a/nextflow.config b/nextflow.config
@@ -61,7 +61,7 @@ params {
     gatkgenotypes_filter        = '--min_GQ "50" --keep_GQ_0_refs --min_percent_alt_in_AD "0.8" --min_total_DP "10" --keep_all_ref'
     max_amb_samples            = 10000000
     max_perc_amb_samples       = 10
-    min_depth                  = 50
+    min_depth                  = 10
     publish_dir_mode           = 'copy'
     rapidnj                    = true
     fasttree                   = true

diff --git a/subworkflows/local/bwa-reference.nf b/subworkflows/local/bwa-reference.nf
@@ -13,6 +13,11 @@ include { SAMTOOLS_FAIDX                  } from '../../modules/nf-core/modules/
 
 process INPUT_PROC {
 
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
+        'quay.io/biocontainers/python:3.8.3' }"
+
     input:
     path(fasta)