Release 0.10.1 (#91)

Author: leahkemp

Dockerfile

@@ -102,7 +102,8 @@ RUN wget https://repo.anaconda.com/miniconda/Miniconda3-py39_25.9.1-3-Linux-x86_
     conda config --add channels conda-forge && \
     conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main && \
     conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r && \
-    conda install -c conda-forge -c bioconda longtr
+    conda install -c conda-forge -c bioconda longtr && \
+    cp /root/miniconda3/bin/LongTR /usr/local/bin/LongTR
 
 # GNU parallel
 RUN wget https://ftp.gnu.org/gnu/parallel/parallel-20191022.tar.bz2 && \
@@ -113,11 +114,10 @@ RUN wget https://ftp.gnu.org/gnu/parallel/parallel-20191022.tar.bz2 && \
     make install
 
 ## deploy env ##
-
 FROM ubuntu:24.04 AS deploy
 LABEL name="pipeface"
 LABEL description="docker image containing most software required for pipeface"
-LABEL version="0.0.2"
+LABEL version="0.0.3"
 LABEL maintainer.name="Leah Kemp"
 LABEL maintainer.email="leahmhkemp@gmail.com"
 
@@ -147,6 +147,7 @@ COPY --from=build \
     /Jasmine/jasmine.jar \
     /Jasmine/jasmine_iris.jar \
     /usr/local/bin/parallel \
+    /usr/local/bin/LongTR \
     /usr/local/bin/
 
 COPY --from=build \
@@ -156,10 +157,3 @@ COPY --from=build \
 COPY --from=build \
     /usr/local/lib/ \
     /usr/local/lib/
-
-COPY --from=build \
-    /root/miniconda3 \
-    /root/miniconda3
-
-# add conda to path
-ENV PATH="/root/miniconda3/bin:${PATH}"

config/nextflow_pipeface_container.config

@@ -36,15 +36,15 @@ process {
         cpus = '1'
         memory = '4GB'
         time = '6h'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'minimap2' {
         queue = ''
         cpus = '16'
         memory = '64GB'
         time = '14h'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'minimod' {
@@ -53,15 +53,15 @@ process {
         memory = '32GB'
         disk = '20GB'
         time = '4h'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'mosdepth' {
         queue = ''
         cpus = '8'
         memory = '32GB'
         time = '2h'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'clair3|clair3_haploid_aware' {
@@ -78,7 +78,7 @@ process {
         cpus = '1'
         memory = '4GB'
         time = '30m'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'clair3_post_processing' {
@@ -87,7 +87,7 @@ process {
         memory = '4GB'
         disk = '10GB'
         time = '30m'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'deepvariant_dry_run' {
@@ -131,7 +131,7 @@ process {
         cpus = '1'
         memory = '4GB'
         time = '1h'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'split_multiallele|split_multiallele_duo|split_multiallele_trio' {
@@ -140,23 +140,23 @@ process {
         memory = '4GB'
         disk = '10GB'
         time = '1h'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'longtr_pre_processing' {
         queue = 'normal'
         cpus = '1'
         memory = '4GB'
         time = '1h'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'longtr|longtr_duo|longtr_trio' {
         queue = ''
         cpus = '96'
         memory = '192GB'
         time = '24h'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'vep_snp_indel|vep_sniffles_sv|vep_cutesv_sv' {
@@ -172,15 +172,15 @@ process {
         cpus = '4'
         memory = '16GB'
         time = '10h'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'whatshap_phase_duo|whatshap_phase_trio' {
         queue = ''
         cpus = '4'
         memory = '16GB'
         time = '36h'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'deeptrio_dry_run' {
@@ -224,7 +224,7 @@ process {
         cpus = '1'
         memory = '4GB'
         time = '1h'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'glnexus_duo|glnexus_trio' {
@@ -240,31 +240,31 @@ process {
         cpus = '1'
         memory = '4GB'
         time = '30m'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'sniffles' {
         queue = ''
         cpus = '4'
         memory = '16GB'
         time = '1h'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'cutesv' {
         queue = ''
         cpus = '8'
         memory = '32GB'
         time = '1h'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
     withName: 'jasmine_sniffles_duo|jasmine_cutesv_duo|jasmine_sniffles_trio|jasmine_cutesv_trio' {
         queue = ''
         cpus = '8'
         memory = '32GB'
         time = '12h'
-        container = 'leahkemp/pipeface:0.0.2'
+        container = 'leahkemp/pipeface:0.0.3'
     }
 
 }

pipeface.nf

@@ -1,7 +1,7 @@
 nextflow.enable.dsl=2
 
 // tag pipeface version
-def pipeface_version = "0.10.0"
+def pipeface_version = "0.10.1"
 
 // create dummy NONE file for optional pipeface inputs
 new File("NONE").text = "Dummy file for optional pipeface inputs. Don't delete during a pipeline run unless you want a bad time.\n"