From 963776cf8197acd091e4600ffbb9bfe41b87730b Mon Sep 17 00:00:00 2001
From: golobor <goloborodko.anton@gmail.com>
Date: Sat, 4 Aug 2018 15:16:31 -0400
Subject: [PATCH] v0.1.0, switch to pairtools, update cooler

---
 CHANGES.md        |  3 +++
 VERSION           |  2 +-
 distiller.nf      | 26 +++++++++++++-------------
 docker/Dockerfile |  1 +
 environment.yml   |  2 +-
 5 files changed, 19 insertions(+), 15 deletions(-)
 create mode 100644 CHANGES.md

diff --git a/CHANGES.md b/CHANGES.md
new file mode 100644
index 0000000..3b3c9d3
--- /dev/null
+++ b/CHANGES.md
@@ -0,0 +1,3 @@
+### 0.1.0 (2018-08-04) ###
+
+* Distiller-env: switch to pairtools v0.2.0 and cooler v0.7.10.
diff --git a/VERSION b/VERSION
index 78a09a8..72290f6 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-version='0.0.11'
+version='0.1.0'
diff --git a/distiller.nf b/distiller.nf
index 4e68571..cedad23 100644
--- a/distiller.nf
+++ b/distiller.nf
@@ -358,11 +358,11 @@ process parse_chunks {
 
     """
     mkdir ./tmp4sort
-    pairsamtools parse ${dropsam_flag} ${dropreadid_flag} ${dropseq_flag} \
+    pairtools parse ${dropsam_flag} ${dropreadid_flag} ${dropseq_flag} \
         -c ${chrom_sizes} ${bam} \
-            | pairsamtools sort --nproc ${task.cpus} \
-                                -o ${library}.${run}.${chunk}.pairsam.${suffix} \
-                                --tmpdir ./tmp4sort \
+            | pairtools sort --nproc ${task.cpus} \
+                             -o ${library}.${run}.${chunk}.pairsam.${suffix} \
+                             --tmpdir ./tmp4sort \
             | cat
 
 
@@ -392,7 +392,7 @@ process merge_chunks_into_runs {
     set library, run, "${library}.${run}.pairsam.${suffix}" into LIB_RUN_PAIRSAMS
  
     script:
-    // can we replace this part with just the "else" branch, so that pairsamtools merge will take care of it?
+    // can we replace this part with just the "else" branch, so that pairtools merge will take care of it?
     if( isSingleFile(pairsam_chunks) )
         """
         ln -s \"\$(readlink -f ${pairsam_chunks})\" ${library}.${run}.pairsam.${suffix}
@@ -400,7 +400,7 @@ process merge_chunks_into_runs {
     else
         """
         mkdir ./tmp4sort
-        pairsamtools merge ${pairsam_chunks} --nproc ${task.cpus} -o ${library}.${run}.pairsam.${suffix} --tmpdir ./tmp4sort
+        pairtools merge ${pairsam_chunks} --nproc ${task.cpus} -o ${library}.${run}.pairsam.${suffix} --tmpdir ./tmp4sort
         rm -rf ./tmp4sort
         """
 
@@ -434,7 +434,7 @@ process merge_runs_into_libraries {
     else
         """
         mkdir ./tmp4sort
-        pairsamtools merge ${run_pairsam} --nproc ${task.cpus} -o ${library}.pairsam.${suffix} --tmpdir ./tmp4sort
+        pairtools merge ${run_pairsam} --nproc ${task.cpus} -o ${library}.pairsam.${suffix} --tmpdir ./tmp4sort
         rm -rf ./tmp4sort
         """
 }
@@ -484,7 +484,7 @@ process filter_make_pairs {
     dropsam = params['map'].get('drop_sam','false').toBoolean()
     if(dropsam) 
         """
-        pairsamtools dedup \
+        pairtools dedup \
             --max-mismatch ${params.filter.pcr_dups_max_mismatch_bp} \
             --mark-dups \
             --output ${library}.nodups.pairs.gz \
@@ -501,21 +501,21 @@ process filter_make_pairs {
         """
     else 
         """
-        pairsamtools dedup \
+        pairtools dedup \
             --max-mismatch ${params.filter.pcr_dups_max_mismatch_bp} \
             --mark-dups \
             --output \
-                >( pairsamtools split \
+                >( pairtools split \
                     --output-pairs ${library}.nodups.pairs.gz \
                     --output-sam ${library}.nodups.bam \
                  ) \
             --output-unmapped \
-                >( pairsamtools split \
+                >( pairtools split \
                     --output-pairs ${library}.unmapped.pairs.gz \
                     --output-sam ${library}.unmapped.bam \
                  ) \
             --output-dups \
-                >( pairsamtools split \
+                >( pairtools split \
                     --output-pairs ${library}.dups.pairs.gz \
                     --output-sam ${library}.dups.bam \
                  ) \
@@ -764,7 +764,7 @@ process merge_stats_libraries_into_groups {
         """
     else
         """
-        pairsamtools stats --merge ${stats} -o ${library_group}.stats
+        pairtools stats --merge ${stats} -o ${library_group}.stats
         """
 }
 
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 9e10a7c..56d4fbe 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -20,6 +20,7 @@ ENV PATH=/miniconda3/bin:${PATH}
 
 # Install conda dependencies
 ADD environment.yml /
+ADD VERSION /
 RUN pwd
 RUN conda config --set always_yes yes --set changeps1 no && \
     conda config --add channels conda-forge && \
diff --git a/environment.yml b/environment.yml
index 52a5bca..667fa07 100644
--- a/environment.yml
+++ b/environment.yml
@@ -21,7 +21,7 @@ dependencies:
     - dask
     - nose 
     - pairix
+    - pairtools
     - pip:
         - cooler>=0.7.1
-        - git+https://github.com/mirnylab/pairsamtools
         - toolz