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Unverified Commit db760f4b authored by Nicolas Servant's avatar Nicolas Servant Committed by GitHub
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Merge pull request #3 from nservant/master

update travis and test-dataset
parents d20ced35 322c97ac
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......@@ -18,10 +18,10 @@ params {
// Digestion Hi-C
restriction_site = 'A^AGCTT'
ligation_site = 'AAGCTAGCTT'
min_restriction_fragment_size = 100
max_restriction_fragment_size = 100000
min_insert_size = 100
max_insert_size = 600
min_restriction_fragment_size =
max_restriction_fragment_size =
min_insert_size =
max_insert_size =
// Hi-C Processing
min_cis_dist =
......
......@@ -9,7 +9,7 @@
params {
config_profile_name = 'Hi-C test data from Dixon et al. (2012)'
config_profile_name = 'Hi-C test data from Schalbetter et al. (2017)'
config_profile_description = 'Minimal test dataset to check pipeline function'
// Limit resources so that this can run on Travis
......@@ -19,10 +19,13 @@ params {
// Input data
readPaths = [
['SRR400264_00', ['https://github.com/nf-core/test-datasets/raw/hic/SRR400264_00_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/SRR400264_00_R2.fastq.gz']],
['SRR400264_01', ['https://github.com/nf-core/test-datasets/raw/hic/SRR400264_01_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/SRR400264_01_R2.fastq.gz']]
['SRR4292758_00', ['https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R2.fastq.gz']]
]
// Annotations
genome = 'GRCh37'
fasta = 'https://github.com/nf-core/test-datasets/raw/hic/reference/W303_SGD_2015_JRIU00000000.fsa'
// Options
skip_cool = true
}
......@@ -33,11 +33,11 @@ def helpMessage() {
Mandatory arguments:
--reads Path to input data (must be surrounded with quotes)
--genome Name of iGenomes reference
-profile Configuration profile to use. Can use multiple (comma separated)
Available: conda, docker, singularity, awsbatch, test and more.
References If not specified in the configuration file or you wish to overwrite any of the references.
--genome Name of iGenomes reference
--bwt2_index Path to Bowtie2 index
--fasta Path to Fasta reference
--chromosome_size Path to chromosome size file
......@@ -72,6 +72,10 @@ def helpMessage() {
--email Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits
-name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
Step options:
--skip_cool Skip generation of cool files
--skip_multiQC Skip MultiQC
AWSBatch options:
--awsqueue The AWSBatch JobQueue that needs to be set when running on AWSBatch
--awsregion The AWS Region for your AWS Batch job to run on
......@@ -138,7 +142,6 @@ if (params.readPaths){
.from( params.readPaths )
.map { row -> [ row[0], [file(row[1][0]), file(row[1][1])]] }
.separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0], a[1][0]), tuple(a[0], a[1][1])] }
.println()
}else{
raw_reads = Channel.create()
......@@ -674,6 +677,9 @@ process generate_cool{
tag "$sample"
publishDir "${params.outdir}/export/cool", mode: 'copy'
when:
!params.skip_cool
input:
set val(sample), file(vpairs) from all_valid_pairs_4cool
file chrsize from chromosome_size_cool.collect()
......@@ -694,6 +700,9 @@ process generate_cool{
process multiqc {
publishDir "${params.outdir}/MultiQC", mode: 'copy'
when:
!params.skip_multiqc
input:
file multiqc_config from ch_multiqc_config
file ('input_*/*') from all_mstats.concat(all_mergestat).collect()
......
......@@ -24,7 +24,8 @@ params {
readPaths = false
chromosome_size = false
restriction_fragments = false
skip_cool = false
skip_multiqc = false
// Boilerplate options
name = false
......
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