Commit cf2262ba authored by Jeremy Mathews's avatar Jeremy Mathews
Browse files

Fix merge conflicts

parents 407ee7d5 aa094631
Pipeline #4414 failed with stages
in 316 minutes and 41 seconds
......@@ -7,6 +7,9 @@ All notable changes to this project will be documented in this file.
- Add Nextflow to references.md
- Fix pool_and_psuedoreplicate.py to run single experiment
- Add test data
- Add PlotProfile Option
- Add Python version to MultiQC
- Add and Update tests
## [publish_1.0.6 ] - 2019-05-31
### Added
......
......@@ -116,6 +116,8 @@ diffPeaks | normcount_peaksets.txt | Use only for replicated samples; peak set v
diffPeaks | pca.pdf | Use only for replicated samples; PCA of peak location and peak intensity
diffPeaks | *_diffbind.bed | Use only for replicated samples; bed file of peak locations between replicates
diffPeaks | *_diffbind.csv | Use only for replicated samples; CSV file of peaks between replicates
plotProfile | plotProfile.png | Plot profile of the TSS region
plotProfile | computeMatrix.gz | Compute Matrix from deeptools to create custom plots other than plotProfile
## Common Quality Control Metrics
+ These are the list of files that should be reviewed before continuing on with the CHIPseq experiment. If your experiment fails any of these metrics, you should pause and re-evaluate whether the data should remain in the study.
......
......@@ -90,6 +90,8 @@ diffPeaks | normcount_peaksets.txt | Use only for replicated samples; peak set v
diffPeaks | pca.pdf | Use only for replicated samples; PCA of peak location and peak intensity
diffPeaks | *_diffbind.bed | Use only for replicated samples; bed file of peak locations between replicates
diffPeaks | *_diffbind.csv | Use only for replicated samples; CSV file of peaks between replicates
plotProfile | plotProfile.png | Plot profile of the TSS region
plotProfile | computeMatrix.gz | Compute Matrix from deeptools to create custom plots other than plotProfile
## Common Quality Control Metrics
+ These are the list of files that should be reviewed before continuing on with the CHIPseq experiment. If your experiment fails any of these metrics, you should pause and re-evaluate whether the data should remain in the study.
......
......@@ -78,21 +78,21 @@ params {
genomesize = 'hs'
chromsizes = '/project/shared/bicf_workflow_ref/GRCh38/genomefile.txt'
fasta = '/project/shared/bicf_workflow_ref/GRCh38/genome.fa'
gta = '/project/shared/bicf_workflow_ref/GRCh38/gencode.gtf'
gtf = '/project/shared/bicf_workflow_ref/GRCh38/gencode.gtf'
}
'GRCh37' {
bwa = '/project/shared/bicf_workflow_ref/GRCh37'
genomesize = 'hs'
chromsizes = '/project/shared/bicf_workflow_ref/GRCh37/genomefile.txt'
fasta = '/project/shared/bicf_workflow_ref/GRCh37/genome.fa'
gta = '/project/shared/bicf_workflow_ref/GRCh37/gencode.gtf'
gtf = '/project/shared/bicf_workflow_ref/GRCh37/gencode.gtf'
}
'GRCm38' {
bwa = '/project/shared/bicf_workflow_ref/GRCm38'
genomesize = 'mm'
chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/genomefile.txt'
fasta = '/project/shared/bicf_workflow_ref/GRCm38/genome.fa'
gta = '/project/shared/bicf_workflow_ref/GRCm38/gencode.gtf'
gtf = '/project/shared/bicf_workflow_ref/GRCm38/gencode.gtf'
}
}
}
......
......@@ -28,7 +28,6 @@ params.skipMotif = false
params.skipPlotProfile = false
params.references = "$baseDir/../docs/references.md"
params.multiqc = "$baseDir/conf/multiqc_config.yaml"
params.gtf = "/project/shared/bicf_workflow_ref/$params.genome/gencode.gtf"
// Assign variables if astrocyte
if (params.astrocyte) {
......@@ -37,6 +36,7 @@ if (params.astrocyte) {
params.bwaIndex = "$referenceLocation/$params.genome"
params.chromSizes = "$referenceLocation/$params.genome/genomefile.txt"
params.fasta = "$referenceLocation/$params.genome/genome.fa"
params.gtf = "$referenceLocation/$params.genome/gencode.gtf"
if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
params.genomeSize = 'hs'
} else if (params.genome == 'GRCm38') {
......@@ -47,6 +47,7 @@ if (params.astrocyte) {
params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
params.gtf = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
}
......@@ -463,13 +464,17 @@ peaksDesign = experimentPeaks
//plotProfile
process plotProfile {
publishDir "$outDir/${task.process}", mode: 'copy'
publishDir "$outDir/experimentQC", mode: 'copy'
input:
file ("*.pooled.fc_signal.bw") from bigwigs.collect()
file gtf from gtfFile
output:
file '*.{png,gz}' into plotProfile
when:
!skipPlotProfile
......
#!/bin/bash
#plotProfile.sh
bws=`ls *.bw`
gtf=`ls *.gtf *.bed`
bws=$(ls *.bw)
gtf=$(ls *.gtf *.bed)
computeMatrix reference-point \
--referencePoint TSS \
......
#!/usr/bin/env python3
import pytest
import os
import utils
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/experimentQC/'
@pytest.mark.singleend
def test_plot_singleend():
assert os.path.exists(os.path.join(test_output_path, 'plotProfile.png'))
@pytest.mark.pairedend
def test_plot_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'computeMatrix.gz'))
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