2 docker containers have been fixed, thanks to Björn

workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga

@@ -103,7 +103,7 @@
     "release": "0.1",
     "name": "Allele-based Pathogen Identification",
     "report": {
-        "markdown": "# Allele-based Pathogen Identification Workflow Report\nBelow are the results for the Allele based Pathogenic Identification Workflow\n\nThis workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Workflow Inputs\nThe Perprocessing workflow main output (Collection of all samples reads after quality retaining and hosts filtering), and a FASTA file of the reference genome of the main Pathogen identified in the Gene based Pathogen Identification workflow, or per-known to the user.\n\n## Workflow Output: \n\n### All variants found per sample against the reference genome\n\n```galaxy\nhistory_dataset_display(output=\"extracted_fields_from_the_vcf_output\")\n```\n\n### Number of variants per sample\n\n```galaxy\nhistory_dataset_display(output=\"number_of_variants_per_sample\")\n```\n\n### Mapping mean depth of coverage per sample\n\n```galaxy\nhistory_dataset_display(output=\"mapping_mean_depth_per_sample\")\n```\n\n### Mapping breadth of coverage per sample\n\n```galaxy\nhistory_dataset_display(output=\"mapping_coverage_percentage_per_sample\")\n```\n\n"
+        "markdown": "# Allele-based Pathogen Identification Workflow Report\nBelow are the results for the Allele based Pathogenic Identification Workflow\n\nThis workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Workflow Inputs\nThe Perprocessing workflow main output (Collection of all samples reads after quality retaining and hosts filtering), and a FASTA file of the reference genome of the main Pathogen identified in the Gene based Pathogen Identification workflow, or per-known to the user.\n\n## Workflow Output: \n\n### All variants found per sample against the reference genome\n\n```galaxy\nhistory_dataset_display(output=\"extracted_fields_from_the_vcf_output\")\n```\n\n### Number of variants per sample\n\n```galaxy\nhistory_dataset_display(output=\"number_of_variants_per_sample\")\n```\n\n### Mapping mean depth of coverage per sample\n\n```galaxy\nhistory_dataset_display(output=\"mapping_mean_depth_per_sample\")\n```\n\n### Mapping breadth of coverage percentage per sample\n\n```galaxy\nhistory_dataset_display(output=\"mapping_coverage_percentage_per_sample\")\n```\n\n"
     },
     "steps": {
         "0": {