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CHANGELOG.md
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# nf-core/hic: Changelog
## v1.1dev
* Fix bug for reads extension _1/_2 (#30)
* Update manual (#28)
## v1.0dev - 2019-04-09
## v1.0 - 2019-05-06
First version of nf-core-hic pipeline which is a Nextflow implementation of the [HiC-Pro pipeline](https://github.com/nservant/HiC-Pro/).
Note that all HiC-Pro functionalities are not yet all implemented. The current version is designed for protocols based on restriction enzyme digestion.
First version of nf-core Hi-C pipeline which is a Nextflow implementation of the [HiC-Pro pipeline](https://github.com/nservant/HiC-Pro/).
Note that all HiC-Pro functionalities are not yet all implemented.
The current version supports most protocols including Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C or HiChip data.
In summary, this version allows :
......
README.md
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# nf-core/hic
# ![nf-core/hic](docs/images/nfcore-hic_logo.png)
**Analysis of Chromosome Conformation Capture data (Hi-C)**.
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From:nfcore/base
Bootstrap:docker
%labels
MAINTAINER Nicolas Servant
DESCRIPTION Singularity image containing all requirements for the nf-core/hic pipeline
VERSION 1.0dev
%environment
PATH=/opt/conda/envs/nf-core-hic-1.0dev/bin:$PATH
export PATH
%files
environment.yml /
%post
/opt/conda/bin/conda env create -f /environment.yml
/opt/conda/bin/conda clean -a
docs/images/nfcore-hic_logo.png
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docs/usage.md
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......@@ -51,6 +51,11 @@
* [`--splitFastq`](#--splitFastq)
* [`--saveReference`](#--saveReference)
* [`--saveAlignedIntermediates`](#--saveAlignedIntermediates)
* [Skip options](#skip-options)
* [--skip_maps](#--skip_maps)
* [--skip_ice](#--skip_ice)
* [--skip_cool](#--skip_cool)
* [--skip_multiqc](#--skip_multiqc)
* [Job resources](#job-resources)
* [Automatic resubmission](#automatic-resubmission)
* [Custom resource requests](#custom-resource-requests)
......@@ -457,6 +462,40 @@ If specified, all intermediate mapping files are saved and exported in the resul
--saveReference
```
## Skip options
#### `--skip_maps`
If defined, the workflow stops with the list of valid interactions, and the genome-wide maps are not built. Usefult for capture-C analysis. Default: false
```bash
--skip_maps
```
#### `--skip_ice`
If defined, the ICE normalization is not run on the raw contact maps. Default: false
```bash
--skip_ice
```
#### `--skip_cool`
If defined, cooler files are not generated. Default: false
```bash
--skip_cool
```
#### `--skip_multiqc`
If defined, the MultiQC report is not generated. Default: false
```bash
--skip_multiqc
```
## Job resources
### Automatic resubmission
Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with an error code of `143` (exceeded requested resources) it will automatically resubmit with higher requests (2 x original, then 3 x original). If it still fails after three times then the pipeline is stopped.
......
main.nf
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......@@ -64,6 +64,7 @@ def helpMessage() {
-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. Default: false
--skip_ice Skip ICE normalization. Default: false
--skip_cool Skip generation of cool files. Default: false
......@@ -666,12 +667,17 @@ process remove_duplicates {
if ( params.rm_dup ){
"""
mkdir -p stats/${sample}
## Sort valid pairs and remove read pairs with same starts (i.e duplicated read pairs)
sort -T /tmp/ -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \
awk -F"\\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=\$2 || c2!=\$5 || s1!=\$3 || s2!=\$6){print;c1=\$2;c2=\$5;s1=\$3;s2=\$6}' > ${sample}.allValidPairs
echo -n "valid_interaction\t" > stats/${sample}/${sample}_allValidPairs.mergestat
cat ${vpairs} | wc -l >> stats/${sample}/${sample}_allValidPairs.mergestat
echo -n "valid_interaction_rmdup\t" >> stats/${sample}/${sample}_allValidPairs.mergestat
cat ${sample}.allValidPairs | wc -l >> stats/${sample}/${sample}_allValidPairs.mergestat
## Count short range (<20000) vs long range contacts
awk 'BEGIN{cis=0;trans=0;sr=0;lr=0} \$2 == \$5{cis=cis+1; d=\$6>\$3?\$6-\$3:\$3-\$6; if (d<=20000){sr=sr+1}else{lr=lr+1}} \$2!=\$5{trans=trans+1}END{print "trans_interaction\\t"trans"\\ncis_interaction\\t"cis"\\ncis_shortRange\\t"sr"\\ncis_longRange\\t"lr}' ${sample}.allValidPairs >> stats/${sample}/${sample}_allValidPairs.mergestat
"""
......@@ -683,6 +689,8 @@ process remove_duplicates {
cat ${vpairs} | wc -l >> stats/${sample}/${sample}_allValidPairs.mergestat
echo -n "valid_interaction_rmdup\t" >> stats/${sample}/${sample}_allValidPairs.mergestat
cat ${sample}.allValidPairs | wc -l >> stats/${sample}/${sample}_allValidPairs.mergestat
## Count short range (<20000) vs long range contacts
awk 'BEGIN{cis=0;trans=0;sr=0;lr=0} \$2 == \$5{cis=cis+1; d=\$6>\$3?\$6-\$3:\$3-\$6; if (d<=20000){sr=sr+1}else{lr=lr+1}} \$2!=\$5{trans=trans+1}END{print "trans_interaction\\t"trans"\\ncis_interaction\\t"cis"\\ncis_shortRange\\t"sr"\\ncis_longRange\\t"lr}' ${sample}.allValidPairs >> stats/${sample}/${sample}_allValidPairs.mergestat
"""
}
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