diff --git a/CHANGELOG.md b/CHANGELOG.md
index b982a5782b737510d5eccd2fe6331c73fd192480..019a0e11fb5808c9d240033171694226a613c5e8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,11 @@
# nf-core/hic: Changelog
+## v1.1dev
+
+* Fix bug for reads extension _1/_2 (#30)
+
+* Update manual (#28)
+
## 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/).
diff --git a/docs/usage.md b/docs/usage.md
index 9b2bb6a5b160dbb19632188ee91c66e58ce58a21..03acd69bbca376826643231be66742d4cc3a28e1 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -85,7 +85,7 @@ NXF_OPTS='-Xms1g -Xmx4g'
The typical command for running the pipeline is as follows:
```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.
diff --git a/main.nf b/main.nf
index eeb692312a671226acc27244bd86c7f8953e6ccb..0d51db3548aff9e55c2f3fd38b5ea9d42e722b57 100644
--- a/main.nf
+++ b/main.nf
@@ -22,57 +22,56 @@ def helpMessage() {
nextflow run nf-core/hic --reads '*_R{1,2}.fastq.gz' -profile conda
Mandatory arguments:
- --reads Path to input data (must be surrounded with quotes)
- -profile Configuration profile to use. Can use multiple (comma separated)
- Available: conda, docker, singularity, awsbatch, test and more.
+ --reads Path to input data (must be surrounded with quotes)
+ -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
- --restriction_fragments Path to restriction fragment file (bed)
+ 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
+ --restriction_fragments Path to restriction fragment file (bed)
Options:
- --bwt2_opts_end2end Options for bowtie2 end-to-end mappinf (first mapping step)
- --bwt2_opts_trimmed Options for bowtie2 mapping after ligation site trimming
- --min_mapq Minimum mapping quality values to consider
-
- --restriction_site Cutting motif(s) of restriction enzyme(s) (comma separated)
- --ligation_site Ligation motifs to trim (comma separated)
- --min_restriction_fragment_size Minimum size of restriction fragments to consider
- --max_restriction_framgnet_size Maximum size of restriction fragmants to consider
- --min_insert_size Minimum insert size of mapped reads to consider
- --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
-
- --min_cis_dist Minimum intra-chromosomal distance to consider
- --rm_singleton Remove singleton reads
- --rm_multi Remove multi-mapped reads
- --rm_dup Remove duplicates
-
- --bin_size Bin size for contact maps (comma separated)
- --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
- --ice_filter_high_count_perc Percentage of high counts columns/rows to filter before ICE normalization
- --ice_eps Convergence criteria for ICE normalization
+ --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. See hic.config for default.
+ --min_mapq Minimum mapping quality values to consider. Default: 10
+ --restriction_site Cutting motif(s) of restriction enzyme(s) (comma separated). Default: 'A^AGCTT'
+ --ligation_site Ligation motifs to trim (comma separated). Default: 'AAGCTAGCTT'
+ --min_restriction_fragment_size Minimum size of restriction fragments to consider. Default: None
+ --max_restriction_framgnet_size Maximum size of restriction fragmants to consider. Default: None
+ --min_insert_size Minimum insert size of mapped reads to consider. Default: None
+ --max_insert_size Maximum insert size of mapped reads to consider. Default: None
+
+ --dnase Run DNase Hi-C mode. All options related to restriction fragments are not considered. Default: false
+
+ --min_cis_dist Minimum intra-chromosomal distance to consider. Default: None
+ --rm_singleton Remove singleton reads. Default: true
+ --rm_multi Remove multi-mapped reads. Default: true
+ --rm_dup Remove duplicates. Default: true
+
+ --bin_size Bin size for contact maps (comma separated). Default: '1000000,500000'
+ --ice_max_iter Maximum number of iteration for ICE normalization. Default: 100
+ --ice_filter_low_count_perc Percentage of low counts columns/rows to filter before ICE normalization. Default: 0.02
+ --ice_filter_high_count_perc Percentage of high counts columns/rows to filter before ICE normalization. Default: 0
+ --ice_eps Convergence criteria for ICE normalization. Default: 0.1
Other options:
- --splitFastq Size of read chuncks to use to speed up the workflow
- --outdir The output directory where the results will be saved
- --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.
+ --splitFastq Size of read chuncks to use to speed up the workflow. Default: None
+ --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. Default: None
+ -name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic. Default: None
Step options:
- --skip_maps Skip generation of contact maps. Useful for capture-C
- --skip_ice Skip ICE normalization
- --skip_cool Skip generation of cool files
- --skip_multiQC Skip MultiQC
+ --skip_maps Skip generation of contact maps. Useful for capture-C. Default: false
+ --skip_ice Skip ICE normalization. Default: false
+ --skip_cool Skip generation of cool files. Default: false
+ --skip_multiQC Skip MultiQC. Default: false
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
+ --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
""".stripIndent()
}
@@ -494,8 +493,8 @@ if (!params.dnase){
set val(oname), file("${prefix}.mapstat") into all_mapstat
script:
- sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2)/
- tag = prefix.toString() =~/_R1|_val_1/ ? "R1" : "R2"
+ sample = prefix.toString() - ~/(_R1$|_R2$|_val_1$|_val_2$|_1$|_2$)/
+ tag = prefix.toString() =~/_R1$|_val_1$|_1$/ ? "R1" : "R2"
oname = prefix.toString() - ~/(\.[0-9]+)$/
"""
@@ -535,8 +534,8 @@ if (!params.dnase){
set val(oname), file("${prefix}.mapstat") into all_mapstat
script:
- sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2)/
- tag = prefix.toString() =~/_R1|_val_1/ ? "R1" : "R2"
+ sample = prefix.toString() - ~/(_R1$|_R2$|_val_1$|_val_2$|_1$|_2$)/
+ tag = prefix.toString() =~/_R1$|_val_1$|_1$/ ? "R1" : "R2"
oname = prefix.toString() - ~/(\.[0-9]+)$/
"""
@@ -552,6 +551,7 @@ if (!params.dnase){
}
}
+
process combine_mapped_files{
tag "$sample = $r1_prefix + $r2_prefix"
publishDir "${params.outdir}/mapping", mode: 'copy',
@@ -699,7 +699,7 @@ process merge_sample {
file("mstats/") into all_mstats
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 =~ /.pairstat/) ){ ext = "mpairstat" }
if ( (fstat =~ /.RSstat/) ){ ext = "mRSstat" }