Merge pull request #36 from nf-core/dev

update from upstream

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/pangenome/pggb:20230113201558a9a04c
+FROM ghcr.io/pangenome/pggb:20230210020215005014
 LABEL authors="Simon Heumos, Michael Heuer, Lukas Heumos, Erik Garrison, Andrea Guarracino" \
       description="Docker image containing all software requirements for the nf-core/pangenome pipeline"
 

README.md

@@ -134,7 +134,7 @@ Many thanks to all who have helped out and contributed along the way, including
 | [Gisela Gabernet](https://github.com/ggabernet)                  | [Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany](https://uni-tuebingen.de/en/research/research-infrastructure/quantitative-biology-center-qbic/)|
 | [Erik Garrison](https://github.com/ekg)                  | [The University of Tennessee Health Science Center, Memphis, Tennessee, TN, USA](https://uthsc.edu/)|
 | [Andrea Guarracino](https://github.com/AndreaGuarracino) | [Genomics Research Centre, Human Technopole, Milan, Italy](https://humantechnopole.it/en/)        |
-| [Friederieke Hanssen](https://github.com/FriederikeHanssen) | [Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany](https://uni-tuebingen.de/en/research/research-infrastructure/quantitative-biology-center-qbic/)        |
+| [Friederike Hanssen](https://github.com/FriederikeHanssen) | [Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany](https://uni-tuebingen.de/en/research/research-infrastructure/quantitative-biology-center-qbic/)        |
 | [Michael Heuer](https://github.com/heuermh)              | [UC Berkeley, USA](https://rise.cs.berkeley.edu)                                      |
 | [Lukas Heumos](https://github.com/zethson)               | [Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany](https://www.helmholtz-muenchen.de/icb/index.html) <br /> [Institute of Lung Biology and Disease and Comprehensive Pneumology Center, Helmholtz Zentrum München, Munich, Germany](https://www.helmholtz-muenchen.de/ilbd/the-institute/cpc/index.html) |
 | [Simon Heumos](https://github.com/subwaystation)         | [Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany](https://uni-tuebingen.de/en/research/research-infrastructure/quantitative-biology-center-qbic/) <br /> [Biomedical Data Science, Department of Computer Science, University of Tübingen, Germany](https://uni-tuebingen.de/en/faculties/faculty-of-science/departments/computer-science/department/) |

bin/native_image.sh

@@ -23,6 +23,8 @@ sed -i "70 s/./#&/" Dockerfile
 sed -i "71 s/./#&/" Dockerfile
 sed -i "72 s/./#&/" Dockerfile
 cp ../pggb/pggb .
+cp ../pggb/partition-before-pggb .
+cp -r ../pggb/scripts .
 if [ ! -d .git ]; then
     cp -r ../pggb/.git .
 fi
@@ -45,6 +47,6 @@ docker build -t ${USER}/pangenome-dev:latest .
 docker run -d -p 5000:5000 --name registry registry:2
 docker image tag $(docker images | grep pangenome-dev | grep latest | grep ${USER} | tr -s ' ' | cut -f 3 -d ' ') localhost:5000/pangenome-dev
 docker push localhost:5000/pangenome-dev
-SINGULARITY_NOHTTPS=true singularity build pangenome-dev.img docker://localhost:5000/pangenome-dev
+SINGULARITY_NOHTTPS=true singularity build --force pangenome-dev.img docker://localhost:5000/pangenome-dev
 docker container stop registry && docker container rm -v registry
 #### SKIP ####

subworkflows/local/odgi/odgi2d/main.nf

@@ -1,4 +1,5 @@
 process odgiLayout {
+  publishDir "${params.outdir}/odgi_layout", mode: "${params.publish_dir_mode}"
   input:
   path(graph)
 

subworkflows/local/pggb/main.nf

@@ -53,9 +53,9 @@ if (params.smoothxg_poa_params == null) {
 def smoothxg_poa_params_display = smoothxg_poa_params.replaceAll(/,/, "_")
 def smoothxg_temp_dir = params.smoothxg_temp_dir ? "-b${params.smoothxg_temp_dir}" : ""
 def smoothxg_keep_intermediate_files = params.smoothxg_keep_intermediate_files ? "-K" : ""
-def smoothxg_xpoa = "-S" 
+def smoothxg_xpoa = "" 
 if (params.smoothxg_run_abpoa != null) {
-  smoothxg_xpoa = ""
+  smoothxg_xpoa = "-A"
 }
 def smoothxg_poa_mode = params.smoothxg_run_global_poa ? "-Z" : ""
 // disabling consensus graph mode cause it is buggy