Merge pull request #116 from apeltzer/dev

2.0.4dev

Author: apeltzer

.travis.yml

@@ -13,7 +13,7 @@ before_install:
   # Pull the docker image first so the test doesn't wait for this
   - docker pull nfcore/eager:dev
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/eager:dev nfcore/eager:2.0.3
+  - docker tag nfcore/eager:dev nfcore/eager:latest
 
 install:
   # Install Nextflow

Dockerfile

@@ -3,4 +3,4 @@ FROM nfcore/base
 LABEL description="Docker image containing all requirements for nf-core/eager pipeline"
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-eager-2.0.3/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.0.4dev/bin:$PATH

Singularity

@@ -4,10 +4,10 @@ Bootstrap:docker
 %labels
     MAINTAINER Alexander Peltzer <alexander.peltzer@qbic.uni-tuebingen.de>
     DESCRIPTION Container image containing all requirements for the nf-core/eager pipeline
-    VERSION 2.0.3
+    VERSION 2.0.4dev
 
 %environment
-    PATH=/opt/conda/envs/nf-core-eager-2.0.3/bin:$PATH
+    PATH=/opt/conda/envs/nf-core-eager-2.0.4dev/bin:$PATH
     export PATH
 
 %files

bin/scrape_software_versions.py

@@ -16,6 +16,7 @@
     'GATK': ['v_gatk.txt', r"Version:([\d\.]+)"],
     'bamUtil' : ['v_bamutil.txt', r"Version: ([\d\.]+)"],
     'fastP': ['v_fastp.txt', r"([\d\.]+)"],
+    'DamageProfiler' : ['v_damageprofiler.txt', r"version\": \"([\d\.]+)"],
 }
 results = OrderedDict()
 results['nf-core/eager'] = '<span style="color:#999999;\">N/A</span>'
@@ -30,6 +31,7 @@
 results['GATK'] = '<span style="color:#999999;\">N/A</span>'
 results['bamUtil'] = '<span style="color:#999999;\">N/A</span>'
 results['fastP'] = '<span style="color:#999999;\">N/A</span>'
+results['DamageProfiler'] = '<span style="color:#999999;\">N/A</span>'
 
 # Search each file using its regex
 for k, v in regexes.items():

environment.yml

@@ -1,4 +1,4 @@
-name: nf-core-eager-2.0.3
+name: nf-core-eager-2.0.4dev
 channels:
   - defaults
   - bioconda
@@ -9,12 +9,12 @@ dependencies:
   - bioconda::adapterremoval=2.2.2
   - bioconda::adapterremovalfixprefix=0.0.4
   - bioconda::bwa=0.7.17
-  - bioconda::picard=2.18.15
+  - bioconda::picard=2.18.21
   - bioconda::samtools=1.9
   - bioconda::dedup=0.12.3
   - bioconda::angsd=0.923
   - bioconda::circularmapper=1.93.4
-  - bioconda::gatk4=4.0.11.0
+  - bioconda::gatk4=4.0.12.0
   - bioconda::qualimap=2.2.2b
   - bioconda::vcf2genome=0.91
   - bioconda::damageprofiler=0.4.4
@@ -25,6 +25,6 @@ dependencies:
   - conda-forge::pigz=2.3.4
   - bioconda::sequencetools=1.2.2
   - bioconda::preseq=2.0.3
-  - bioconda::fastp=0.19.4
+  - bioconda::fastp=0.19.5
   - bioconda::bamutil=1.0.14
   #Missing Schmutzi,snpAD

main.nf

@@ -372,35 +372,6 @@ ${summary.collect { k,v -> "            <dt>$k</dt><dd><samp>${v ?: '<span style
 }
 
 
-/*
- * Parse software version numbers
- */
-process get_software_versions {
-
-    output:
-    file 'software_versions_mqc.yaml' into software_versions_yaml
-
-    script:
-    """
-    echo $workflow.manifest.version &> v_pipeline.txt
-    echo $workflow.nextflow.version &> v_nextflow.txt
-    fastqc --version &> v_fastqc.txt 2>&1 || true
-    multiqc --version &> v_multiqc.txt 2>&1 || true
-    bwa &> v_bwa.txt 2>&1 || true
-    samtools --version &> v_samtools.txt 2>&1 || true
-    AdapterRemoval -version  &> v_adapterremoval.txt 2>&1 || true
-    picard MarkDuplicates --version &> v_markduplicates.txt  2>&1 || true
-    dedup -v &> v_dedup.txt 2>&1 || true
-    preseq &> v_preseq.txt 2>&1 || true
-    gatk BaseRecalibrator --version 2>&1 | grep Version: > v_gatk.txt 2>&1 || true
-    vcf2genome &> v_vcf2genome.txt 2>&1 || true
-    fastp --version &> v_fastp.txt 2>&1 || true
-    bam --version &> v_bamutil.txt 2>&1 || true
-    qualimap --version &> v_qualimap.txt 2>&1 || true
-    
-    scrape_software_versions.py &> software_versions_mqc.yaml
-    """
-}
 
 /* 
 * Create BWA indices if they are not present
@@ -615,7 +586,7 @@ process bwa {
 
     output:
     file "*.sorted.bam" into ch_mapped_reads_idxstats,ch_mapped_reads_filter,ch_mapped_reads_preseq, ch_mapped_reads_damageprofiler
-    file "*.bai" 
+    file "*.bai" into ch_bam_index_for_damageprofiler
 
 
     script:
@@ -868,9 +839,12 @@ process damageprofiler {
     input:
     file bam from ch_mapped_reads_damageprofiler.mix(ch_mapped_reads_damageprofiler_cm,ch_bwamem_mapped_reads_damageprofiler)
     file fasta from ch_fasta_for_damageprofiler
+    file bai from ch_bam_index_for_damageprofiler
+    
 
     output:
-    file "*.json" into ch_damageprofiler_results
+    file "*"
+    file "*/*.json" into ch_damageprofiler_results, ch_damageprofiler_for_software_versions
 
     script:
     """
@@ -1029,6 +1003,63 @@ Downstream VCF tools:
 
 
 
+
+
+
+/*
+ * STEP 3 - Output Description HTML
+ */
+process output_documentation {
+    publishDir "${params.outdir}/Documentation", mode: 'copy'
+
+    input:
+    file output_docs from ch_output_docs
+
+    output:
+    file "results_description.html"
+
+    script:
+    """
+    markdown_to_html.r $output_docs results_description.html
+    """
+}
+
+
+/*
+ * Parse software version numbers
+ */
+process get_software_versions {
+
+    input:
+    file json from ch_damageprofiler_for_software_versions
+
+    output:
+    file 'software_versions_mqc.yaml' into software_versions_yaml
+
+    script:
+    """
+    echo $workflow.manifest.version &> v_pipeline.txt
+    echo $workflow.nextflow.version &> v_nextflow.txt
+    fastqc --version &> v_fastqc.txt 2>&1 || true
+    multiqc --version &> v_multiqc.txt 2>&1 || true
+    bwa &> v_bwa.txt 2>&1 || true
+    samtools --version &> v_samtools.txt 2>&1 || true
+    AdapterRemoval -version  &> v_adapterremoval.txt 2>&1 || true
+    picard MarkDuplicates --version &> v_markduplicates.txt  2>&1 || true
+    dedup -v &> v_dedup.txt 2>&1 || true
+    preseq &> v_preseq.txt 2>&1 || true
+    gatk BaseRecalibrator --version 2>&1 | grep Version: > v_gatk.txt 2>&1 || true
+    vcf2genome &> v_vcf2genome.txt 2>&1 || true
+    fastp --version &> v_fastp.txt 2>&1 || true
+    bam --version &> v_bamutil.txt 2>&1 || true
+    qualimap --version &> v_qualimap.txt 2>&1 || true
+    cat $json &> v_damageprofiler.txt 2>&1 || true 
+    
+    scrape_software_versions.py &> software_versions_mqc.yaml
+    """
+}
+
+
 /*
  * STEP 2 - MultiQC
  */
@@ -1065,26 +1096,6 @@ process multiqc {
 
 
 
-/*
- * STEP 3 - Output Description HTML
- */
-process output_documentation {
-    publishDir "${params.outdir}/Documentation", mode: 'copy'
-
-    input:
-    file output_docs from ch_output_docs
-
-    output:
-    file "results_description.html"
-
-    script:
-    """
-    markdown_to_html.r $output_docs results_description.html
-    """
-}
-
-
-
 
 /*
  * Completion e-mail notification

nextflow.config

@@ -10,7 +10,7 @@
 
 // Global default params, used in configs
 params {
-  container = 'nfcore/eager:2.0.3'
+  container = 'nfcore/eager:latest'
 
   //Pipeline options
   aligner = 'bwa'
@@ -107,7 +107,7 @@ manifest {
   name = 'nf-core/eager'
   author = 'Alexander Peltzer, Stephen Clayton, James A Fellows-Yates'
   homePage = 'https://github.com/nf-core/eager'
-  version = '2.0.3'
+  version = '2.0.4dev'
   description = 'A fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support.'
   mainScript = 'main.nf'
   nextflowVersion = '>=0.32.0'