From 49e72d8281f0a6ebe465ee5badecf3ff09822b51 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 3 May 2019 15:16:03 +0200
Subject: [PATCH 1/5] Add hic logo with proper fonts

---
 README.md                |   2 +-
 docs/images/hic_logo.svg | 205 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 206 insertions(+), 1 deletion(-)
 create mode 100644 docs/images/hic_logo.svg

diff --git a/README.md b/README.md
index 5f2c074..7a11aa6 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# nf-core/hic
+# ![nf-core/hic](docs/images/hic_logo.svg)
 
 **Analysis of Chromosome Conformation Capture data (Hi-C)**.
 
diff --git a/docs/images/hic_logo.svg b/docs/images/hic_logo.svg
new file mode 100644
index 0000000..7a20869
--- /dev/null
+++ b/docs/images/hic_logo.svg
@@ -0,0 +1,205 @@
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From 2e2f93af95cbf4c217f701a507e00d6111cb8117 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 3 May 2019 15:16:37 +0200
Subject: [PATCH 2/5] Remove old logo

---
 docs/images/nfcore-hic_logo.png | Bin 12952 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 docs/images/nfcore-hic_logo.png

diff --git a/docs/images/nfcore-hic_logo.png b/docs/images/nfcore-hic_logo.png
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From 85a72646f31b462759bbf328861cd245fcab6ae6 Mon Sep 17 00:00:00 2001
From: nservant <nservant@curie.fr>
Date: Mon, 6 May 2019 17:36:51 +0200
Subject: [PATCH 3/5] update doc with skip options

---
 docs/usage.md | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/docs/usage.md b/docs/usage.md
index 9b2bb6a..d166cf6 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.

From 2a742e16bee3cd514926f4bbe269904b18963420 Mon Sep 17 00:00:00 2001
From: nservant <nservant@curie.fr>
Date: Mon, 6 May 2019 17:37:02 +0200
Subject: [PATCH 4/5] add comments on rm_dup

---
 main.nf | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index eeb6923..ce29fd5 100644
--- a/main.nf
+++ b/main.nf
@@ -67,7 +67,7 @@ def helpMessage() {
     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_cool			    Skip generation of cooler files
       --skip_multiQC			    Skip MultiQC
 
     AWSBatch options:
@@ -666,12 +666,17 @@ 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 +688,8 @@ 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
    """
    }

From 05f19b075ff2f629fe1ddede92da650153d73dae Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 6 May 2019 17:53:10 +0200
Subject: [PATCH 5/5] Polish release

---
 README.md                                     |   2 +-
 Singularity                                   |  18 ------------------
 docs/images/nfcore-hic_logo.png               | Bin 0 -> 12198 bytes
 .../{hic_logo.svg => nfcore-hic_logo.svg}     |   0
 4 files changed, 1 insertion(+), 19 deletions(-)
 delete mode 100644 Singularity
 create mode 100644 docs/images/nfcore-hic_logo.png
 rename docs/images/{hic_logo.svg => nfcore-hic_logo.svg} (100%)

diff --git a/README.md b/README.md
index 7a11aa6..37692cf 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# ![nf-core/hic](docs/images/hic_logo.svg)
+# ![nf-core/hic](docs/images/nfcore-hic_logo.png)
 
 **Analysis of Chromosome Conformation Capture data (Hi-C)**.
 
diff --git a/Singularity b/Singularity
deleted file mode 100644
index 927866f..0000000
--- 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
new file mode 100644
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diff --git a/docs/images/hic_logo.svg b/docs/images/nfcore-hic_logo.svg
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