diff --git a/Dockerfile b/Dockerfile index 61ac8872..9b6af64a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/pangenome/pggb:2022092009132668cb88 +FROM ghcr.io/pangenome/pggb:2022092217355879ede8 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" diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml index 779d97b4..c2d56baa 100644 --- a/assets/multiqc_config.yaml +++ b/assets/multiqc_config.yaml @@ -1,5 +1,8 @@ # Report section config for nice titles and descriptions custom_data: + odgi_O: + section_name: ODGI Compressed 1D visualization + description: This image shows a 1D rendering of the built pangenome graph. The graph nodes are arranged from left to right, forming the pangenome sequence. Summarization of path coverage across all paths. A heatmap color-coding from https://colorbrewer2.org/#type=diverging&scheme=RdBu&n=11 is used. Dark blue means highest coverage. Dark red means lowest coverage. The path names are placed on the left. The black lines under the paths are the links, which represent the graph topology. odgi_viz: section_name: ODGI 1D visualization description: This image shows a 1D rendering of the built pangenome graph. The graph nodes are arranged from left to right, forming the pangenome sequence. The colored bars represent the paths versus the pangenome sequence in a binary matrix. The path names are placed on the left. The black lines under the paths are the links, which represent the graph topology. @@ -18,6 +21,8 @@ custom_data: # Custom search patterns to find the image outputs sp: + odgi_O: + fn: "*O_multiqc.png" odgi_draw: fn: "*draw_multiqc.png" odgi_viz: @@ -40,6 +45,7 @@ module_order: # Set the order that the custom content plots should come in custom_content: order: + - odgi_O - odgi_viz - odgi_viz_pos - odgi_viz_inv diff --git a/main.nf b/main.nf index acd46e43..6b57f499 100644 --- a/main.nf +++ b/main.nf @@ -405,6 +405,7 @@ process odgiViz { odgi viz -i $graph -o ${graph}.viz_pos_multiqc.png -x 1500 -y 500 -a 10 -I ${params.smoothxg_consensus_prefix} -u -d odgi viz -i $graph -o ${graph}.viz_depth_multiqc.png -x 1500 -y 500 -a 10 -I ${params.smoothxg_consensus_prefix} -m odgi viz -i $graph -o ${graph}.viz_inv_multiqc.png -x 1500 -y 500 -a 10 -I ${params.smoothxg_consensus_prefix} -z + odgi viz -i $graph -o ${graph}.viz_O_multiqc.png -x 1500 -y 500 -a 10 -I ${params.smoothxg_consensus_prefix} -O """ }