Merge pull request #1 from TRON-Bioinformatics/fixes

fix R version for sequenza + hard code VROOM size

Author: priesgo

.github/workflows/automated_tests.yml

@@ -14,20 +14,31 @@ jobs:
       with:
         distribution: 'zulu' # See 'Supported distributions' for available options
         java-version: '11'
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        auto-update-conda: true
-        channels: defaults,conda-forge,bioconda,r
     - name: Install dependencies
       run: |
-        apt-get update && apt-get --assume-yes install wget make procps software-properties-common
+        apt-get -q update && apt-get -q --assume-yes install wget make procps software-properties-common
         wget -qO- https://get.nextflow.io | bash && cp nextflow /usr/local/bin/nextflow
-    - name: Cache conda environments
-      uses: actions/cache@v2
-      with:
-        path: |
-          /home/runner/work/tronflow-cnvkit/tronflow-cnvkit/work/conda
-        key: ${{ runner.os }}-tronflow-cnvkit
+        wget -qO Mambaforge.sh  "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
+        bash Mambaforge.sh -b -p "${HOME}/conda"
+        source "${HOME}/conda/etc/profile.d/conda.sh"
+        conda activate
+        source "${HOME}/conda/etc/profile.d/mamba.sh"
+        export PATH="${HOME}/conda/bin:${PATH}"
+        echo $PATH
+        # this is a workaround for https://github.com/mamba-org/mamba/issues/1993
+        echo "use_lockfiles: false" >> ~/.condarc
+        echo "channels:" >> ~/.condarc
+        echo "  - defaults" >> ~/.condarc
+        echo "  - conda-forge" >> ~/.condarc
+        echo "  - bioconda" >> ~/.condarc
+    #- name: Cache conda environments
+    #  uses: actions/cache@v2
+    #  with:
+    #    path: |
+    #      /home/runner/work/tronflow-cnvkit/tronflow-cnvkit/work/conda
+    #    key: ${{ runner.os }}-tronflow-cnvkit
     - name: Run tests
       run: |
+        export PATH="${HOME}/conda/bin:${PATH}"
+        echo $PATH
         make

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "modules"]
 	path = modules
-	url = https://github.com/nf-core/modules
+	url = https://github.com/tron-bioinformatics/modules

local_modules/sequenza.nf

@@ -28,7 +28,7 @@ process SEQUENZAUTILS_SEQZBINNING {
 process SEQUENZA_R {
     tag "$meta.id"
 
-    conda (params.enable_conda ? "bioconda::r-sequenza=3.0.0" : null)
+    conda (params.enable_conda ? "conda-forge::r-base=4.2.2 bioconda::r-sequenza=3.0.0" : null)
 
     input:
     tuple val(meta), path(seqz)
@@ -42,7 +42,7 @@ process SEQUENZA_R {
 
     library(sequenza)
 
-    Sys.setenv(VROOM_CONNECTION_SIZE = "${params.VROOM_CONNECTION_SIZE}")
+    Sys.setenv(VROOM_CONNECTION_SIZE = "131072000")
 
     seqz <- sequenza.extract(file="${seqz}", verbose = FALSE)
     #data.file <-  system.file("extdata", "example.seqz.txt.gz", package = "sequenza")

main.nf

@@ -3,9 +3,9 @@
 
 nextflow.enable.dsl = 2
 
-include { CNVKIT_BATCH } from './modules/modules/cnvkit/batch/main'
-include { SEQUENZAUTILS_GCWIGGLE } from './modules/modules/sequenzautils/gcwiggle/main'
-include { SEQUENZAUTILS_BAM2SEQZ } from './modules/modules/sequenzautils/bam2seqz/main'
+include { CNVKIT_BATCH } from './modules/modules/nf-core/cnvkit/batch/main'
+include { SEQUENZAUTILS_GCWIGGLE } from './modules/modules/nf-core/sequenzautils/gcwiggle/main'
+include { SEQUENZAUTILS_BAM2SEQZ } from './modules/modules/nf-core/sequenzautils/bam2seqz/main'
 include { SEQUENZAUTILS_SEQZBINNING; SEQUENZA_R } from './local_modules/sequenza'
 
 
@@ -74,7 +74,7 @@ workflow {
 
     if (!params.skip_cnvkit) {
         // NOTE: it does not provide fasta.fai or CNVkit reference, but these are created every time
-        CNVKIT_BATCH(merged_bams, params.reference, [], params.intervals, [])
+        CNVKIT_BATCH(merged_bams, params.reference, [], params.intervals, [], false)
     }
 
     if (!params.skip_sequenza) {

modules

@@ -48,13 +48,19 @@ process {
 profiles {
   conda {
     params.enable_conda = true
-    conda { createTimeout = "120 min" }
+    conda.enabled = true
+    conda.createTimeout = "120 min"
+  }
+  mamba {
+    params.enable_conda = true
+    conda.enabled = true
+    conda.createTimeout = "120 min"
+    conda.useMamba = true
   }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   test {
-    params.reference = "$baseDir/test_data/ucsc.hg19.minimal.fasta"
-    params.intervals = "$baseDir/test_data/minimal_intervals.bed"
-    params.skip_sequenza = true
+    params.reference = "$baseDir/test_data/Homo_sapiens_assembly38.chr6_22.fasta.gz"
+    params.intervals = "$baseDir/test_data/Exome-Agilent_V6.hg38.chr6_chr22.bed"
     timeline.enabled = false
     report.enabled = false
     trace.enabled = false
@@ -72,7 +78,7 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 
 cleanup = true
 
-VERSION = '0.2.1'
+VERSION = '0.2.2'
 DOI = 'doi'
 
 manifest {