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Commit 8769ed0c authored by nservant's avatar nservant
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fix issue #28 #30

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CHANGELOG.md
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# nf-core/hic: Changelog # nf-core/hic: Changelog
## v1.1dev
* Fix bug for reads extension _1/_2 (#30)
* Update manual (#28)
## v1.0dev - 2019-04-09 ## v1.0dev - 2019-04-09
First version of nf-core-hic pipeline which is a Nextflow implementation of the [HiC-Pro pipeline](https://github.com/nservant/HiC-Pro/). First version of nf-core-hic pipeline which is a Nextflow implementation of the [HiC-Pro pipeline](https://github.com/nservant/HiC-Pro/).
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docs/usage.md
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...@@ -85,7 +85,7 @@ NXF_OPTS='-Xms1g -Xmx4g' ...@@ -85,7 +85,7 @@ NXF_OPTS='-Xms1g -Xmx4g'
The typical command for running the pipeline is as follows: The typical command for running the pipeline is as follows:
```bash ```bash
nextflow run nf-core/hic --reads '*_R{1,2}.fastq.gz' -genome GRCh37 -profile docker nextflow run nf-core/hic --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -profile docker
``` ```
This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
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main.nf
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...@@ -22,57 +22,56 @@ def helpMessage() { ...@@ -22,57 +22,56 @@ def helpMessage() {
nextflow run nf-core/hic --reads '*_R{1,2}.fastq.gz' -profile conda nextflow run nf-core/hic --reads '*_R{1,2}.fastq.gz' -profile conda
Mandatory arguments: Mandatory arguments:
--reads Path to input data (must be surrounded with quotes) --reads Path to input data (must be surrounded with quotes)
-profile Configuration profile to use. Can use multiple (comma separated) -profile Configuration profile to use. Can use multiple (comma separated)
Available: conda, docker, singularity, awsbatch, test and more. 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. References: If not specified in the configuration file or you wish to overwrite any of the references.
--genome Name of iGenomes reference --genome Name of iGenomes reference
--bwt2_index Path to Bowtie2 index --bwt2_index Path to Bowtie2 index
--fasta Path to Fasta reference --fasta Path to Fasta reference
--chromosome_size Path to chromosome size file --chromosome_size Path to chromosome size file
--restriction_fragments Path to restriction fragment file (bed) --restriction_fragments Path to restriction fragment file (bed)
Options: Options:
--bwt2_opts_end2end Options for bowtie2 end-to-end mappinf (first mapping step) --bwt2_opts_end2end Options for bowtie2 end-to-end mappinf (first mapping step). See hic.config for default.
--bwt2_opts_trimmed Options for bowtie2 mapping after ligation site trimming --bwt2_opts_trimmed Options for bowtie2 mapping after ligation site trimming. See hic.config for default.
--min_mapq Minimum mapping quality values to consider --min_mapq Minimum mapping quality values to consider. Default: 10
--restriction_site Cutting motif(s) of restriction enzyme(s) (comma separated). Default: 'A^AGCTT'
--restriction_site Cutting motif(s) of restriction enzyme(s) (comma separated) --ligation_site Ligation motifs to trim (comma separated). Default: 'AAGCTAGCTT'
--ligation_site Ligation motifs to trim (comma separated) --min_restriction_fragment_size Minimum size of restriction fragments to consider. Default: None
--min_restriction_fragment_size Minimum size of restriction fragments to consider --max_restriction_framgnet_size Maximum size of restriction fragmants to consider. Default: None
--max_restriction_framgnet_size Maximum size of restriction fragmants to consider --min_insert_size Minimum insert size of mapped reads to consider. Default: None
--min_insert_size Minimum insert size of mapped reads to consider --max_insert_size Maximum insert size of mapped reads to consider. Default: None
--max_insert_size Maximum insert size of mapped reads to consider
--dnase Run DNase Hi-C mode. All options related to restriction fragments are not considered. Default: false
--dnase Run DNase Hi-C mode. All options related to restriction fragments are not considered
--min_cis_dist Minimum intra-chromosomal distance to consider. Default: None
--min_cis_dist Minimum intra-chromosomal distance to consider --rm_singleton Remove singleton reads. Default: true
--rm_singleton Remove singleton reads --rm_multi Remove multi-mapped reads. Default: true
--rm_multi Remove multi-mapped reads --rm_dup Remove duplicates. Default: true
--rm_dup Remove duplicates
--bin_size Bin size for contact maps (comma separated). Default: '1000000,500000'
--bin_size Bin size for contact maps (comma separated) --ice_max_iter Maximum number of iteration for ICE normalization. Default: 100
--ice_max_iter Maximum number of iteration for ICE normalization --ice_filter_low_count_perc Percentage of low counts columns/rows to filter before ICE normalization. Default: 0.02
--ice_filter_low_count_perc Percentage of low counts columns/rows to filter before ICE normalization --ice_filter_high_count_perc Percentage of high counts columns/rows to filter before ICE normalization. Default: 0
--ice_filter_high_count_perc Percentage of high counts columns/rows to filter before ICE normalization --ice_eps Convergence criteria for ICE normalization. Default: 0.1
--ice_eps Convergence criteria for ICE normalization
Other options: Other options:
--splitFastq Size of read chuncks to use to speed up the workflow --splitFastq Size of read chuncks to use to speed up the workflow. Default: None
--outdir The output directory where the results will be saved --outdir The output directory where the results will be saved. Default: './results'
--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 --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. Default: None
-name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic. -name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic. Default: None
Step options: Step options:
--skip_maps Skip generation of contact maps. Useful for capture-C --skip_maps Skip generation of contact maps. Useful for capture-C. Default: false
--skip_ice Skip ICE normalization --skip_ice Skip ICE normalization. Default: false
--skip_cool Skip generation of cool files --skip_cool Skip generation of cool files. Default: false
--skip_multiQC Skip MultiQC --skip_multiQC Skip MultiQC. Default: false
AWSBatch options: AWSBatch options:
--awsqueue The AWSBatch JobQueue that needs to be set when running on AWSBatch --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 --awsregion The AWS Region for your AWS Batch job to run on
""".stripIndent() """.stripIndent()
} }
...@@ -494,8 +493,8 @@ if (!params.dnase){ ...@@ -494,8 +493,8 @@ if (!params.dnase){
set val(oname), file("${prefix}.mapstat") into all_mapstat set val(oname), file("${prefix}.mapstat") into all_mapstat
script: script:
sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2)/ sample = prefix.toString() - ~/(_R1$|_R2$|_val_1$|_val_2$|_1$|_2$)/
tag = prefix.toString() =~/_R1|_val_1/ ? "R1" : "R2" tag = prefix.toString() =~/_R1$|_val_1$|_1$/ ? "R1" : "R2"
oname = prefix.toString() - ~/(\.[0-9]+)$/ oname = prefix.toString() - ~/(\.[0-9]+)$/
""" """
...@@ -535,8 +534,8 @@ if (!params.dnase){ ...@@ -535,8 +534,8 @@ if (!params.dnase){
set val(oname), file("${prefix}.mapstat") into all_mapstat set val(oname), file("${prefix}.mapstat") into all_mapstat
script: script:
sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2)/ sample = prefix.toString() - ~/(_R1$|_R2$|_val_1$|_val_2$|_1$|_2$)/
tag = prefix.toString() =~/_R1|_val_1/ ? "R1" : "R2" tag = prefix.toString() =~/_R1$|_val_1$|_1$/ ? "R1" : "R2"
oname = prefix.toString() - ~/(\.[0-9]+)$/ oname = prefix.toString() - ~/(\.[0-9]+)$/
""" """
...@@ -552,6 +551,7 @@ if (!params.dnase){ ...@@ -552,6 +551,7 @@ if (!params.dnase){
} }
} }
process combine_mapped_files{ process combine_mapped_files{
tag "$sample = $r1_prefix + $r2_prefix" tag "$sample = $r1_prefix + $r2_prefix"
publishDir "${params.outdir}/mapping", mode: 'copy', publishDir "${params.outdir}/mapping", mode: 'copy',
...@@ -699,7 +699,7 @@ process merge_sample { ...@@ -699,7 +699,7 @@ process merge_sample {
file("mstats/") into all_mstats file("mstats/") into all_mstats
script: script:
sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2)/ sample = prefix.toString() - ~/(_R1$|_R2$|_val_1$|_val_2$|_1$|_2$)/
if ( (fstat =~ /.mapstat/) ){ ext = "mmapstat" } if ( (fstat =~ /.mapstat/) ){ ext = "mmapstat" }
if ( (fstat =~ /.pairstat/) ){ ext = "mpairstat" } if ( (fstat =~ /.pairstat/) ){ ext = "mpairstat" }
if ( (fstat =~ /.RSstat/) ){ ext = "mRSstat" } if ( (fstat =~ /.RSstat/) ){ ext = "mRSstat" }
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