diff --git a/CHANGELOG.md b/CHANGELOG.md
index 019a0e11fb5808c9d240033171694226a613c5e8..39ad52a5dad8332451ef7a68cf2fa1ce902646f6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,15 +1,17 @@
# 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 :
diff --git a/README.md b/README.md
index 5f2c07459b0e8da3644198705f6ecb91b57bca01..37692cf5d7e8901feeb77f29da73ad500ca46cc4 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# nf-core/hic
+# 
**Analysis of Chromosome Conformation Capture data (Hi-C)**.
diff --git a/Singularity b/Singularity
deleted file mode 100644
index 927866f0ec891fab132980e50a91d78d7f887eaa..0000000000000000000000000000000000000000
--- a/Singularity
+++ /dev/null
@@ -1,18 +0,0 @@
-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
diff --git a/docs/images/nfcore-hic_logo.png b/docs/images/nfcore-hic_logo.png
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new file mode 100644
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diff --git a/docs/usage.md b/docs/usage.md
index 03acd69bbca376826643231be66742d4cc3a28e1..53d922a2fddf53e8b3924b16f7edc3fe97464d73 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -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.
diff --git a/main.nf b/main.nf
index 0d51db3548aff9e55c2f3fd38b5ea9d42e722b57..1bd5a3a821f01b05887aa3dc1fefbee47a58fc34 100644
--- a/main.nf
+++ b/main.nf
@@ -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
"""
}