Merge branch 'devel' of git.lumc.nl:hem/hamlet into devel

Snakefile

@@ -14,9 +14,9 @@ localrules: create_summary, generate_report, package_results
 
 containers = {
     "fsnviz": "docker://quay.io/biocontainers/fsnviz:0.3.0--py_3",
-    "hamlet-scripts": "docker://lumc/hamlet-scripts:0.3",
+    "hamlet-scripts": "docker://quay.io/redmar_van_den_berg/hamlet-scripts:0.3",
     "debian": "docker://debian:buster-slim",
-    "zip": "docker://lumc/zip:3.0"
+    "zip": "docker://quay.io/redmar_van_den_berg/zip:3.0"
 }
 
 settings=config["settings"]

includes/expression/Snakefile

@@ -11,7 +11,7 @@ containers = {
     "bedtools-2.17-python-2.7": "docker://quay.io/biocontainers/mulled-v2-a9ddcbd438a66450297b5e0b61ac390ee9bfdb61:e60f3cfda0dfcf4a72f2091c6fa1ebe5a5400220-0",
     "htseq": "docker://quay.io/biocontainers/htseq:0.11.2--py27h637b7d7_1",
     "picard": "docker://quay.io/biocontainers/picard:2.20.5--0",
-    "hamlet-scripts": "docker://lumc/hamlet-scripts:0.2"
+    "hamlet-scripts": "docker://quay.io/redmar_van_den_berg/hamlet-scripts:0.2"
 }
 
 settings=config["settings"]

includes/fusion/Snakefile

@@ -12,7 +12,7 @@ containers = {
     "fuma": "docker://quay.io/biocontainers/fuma:3.0.5--py27h24bf2e0_1",
     "fusioncatcher": "docker://quay.io/biocontainers/fusioncatcher:1.20--2",
     "star-fusion": "docker://quay.io/biocontainers/star-fusion:1.6.0--1",
-    "hamlet-scripts": "docker://lumc/hamlet-scripts:0.2"
+    "hamlet-scripts": "docker://quay.io/redmar_van_den_berg/hamlet-scripts:0.2"
 }
 
 settings=config["settings"]

includes/itd/Snakefile.flt3

@@ -4,7 +4,7 @@ from os import path
 
 containers = {
     "bwa-0.7.17-samtools-1.3.1-picard-2.9.2": "docker://quay.io/biocontainers/mulled-v2-1c6be8ad49e4dfe8ab70558e8fb200d7b2fd7509:5900b4e68c4051137fffd99165b00e98f810acae-0",
-    "rose": "docker://lumc/rose-dt:0.4"
+    "rose": "docker://quay.io/redmar_van_den_berg/rose-dt:0.4"
 }
 
 settings=config["settings"]

includes/itd/Snakefile.kmt2a

@@ -2,7 +2,7 @@ from os import path
 
 containers = {
     "bwa-0.7.17-samtools-1.3.1-picard-2.9.2": "docker://quay.io/biocontainers/mulled-v2-1c6be8ad49e4dfe8ab70558e8fb200d7b2fd7509:5900b4e68c4051137fffd99165b00e98f810acae-0",
-    "rose": "docker://lumc/rose-dt:0.4"
+    "rose": "docker://quay.io/redmar_van_den_berg/rose-dt:0.4"
 }
 
 settings=config["settings"]

includes/snv-indels/Snakefile

@@ -9,7 +9,7 @@ containers = {
     "bedtools-2.27-grep-2.14-gawk-5.0-click-7-python-3.7": "docker://quay.io/biocontainers/mulled-v2-a4b89e0b16b1d7db92e5a069e5c40405b3b53aab:98c4ac2f0e27869be58f6a4d8bb7ae3bc02a3a70-0",
     "debian": "docker://debian:buster-slim",
     "gsnap": "docker://quay.io/biocontainers/gmap:2020.06.30--pl526h2f06484_0",
-    "hamlet-scripts": "docker://lumc/hamlet-scripts:0.2",
+    "hamlet-scripts": "docker://quay.io/redmar_van_den_berg/hamlet-scripts:0.2",
     "picard": "docker://quay.io/biocontainers/picard:2.20.5--0",
     "python3": "docker://python:3.7.4-slim-stretch",
     "samtools": "docker://quay.io/biocontainers/samtools:1.6--h244ad75_4",