uodate docker and typos

Author: t-whalley

.gitignore

@@ -3,4 +3,5 @@
 work/
 singularity/*img
 trace*
-
+output/
+outputs/

docker/Dockerfile.ntmprofiler-0.9.9

@@ -41,7 +41,7 @@ RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest| tar -xvj bin
 # install tb-profiler via bioconda; install into 'base' conda env
 RUN micromamba install --yes --name base --channel conda-forge --channel bioconda  \
     ntm-profiler=${NTMPROFILER_VER}
-
+RUN micromamba install --yes --name base --channel conda-forge jq
 # hardcode 'base' env bin into PATH, so conda env does not have to be "activated" at run time
 ENV PATH="/opt/conda/bin:${PATH}"
 

modules/vcfpredictModules.nf

@@ -123,7 +123,7 @@ process ntmprofiler {
     tuple val(sample_name), path(fq1), path(fq2), path(report_json), val(isSampleTB)
 
     output:
-    path("${sample_name}.ntmprofiler-out.json"), path("${sample_name}_report.json"), emit: ntmprofiler_json
+    tuple val(sample_name), path("${sample_name}.ntmprofiler-out.json"), path("${sample_name}_report.json"), emit: ntmprofiler_json
     path("${sample_name}.results.json"), emit: collate_json
 
     when:
@@ -137,7 +137,7 @@ process ntmprofiler {
     mkdir tmp
     ntm-profiler profile -1 $fq1 -2 $fq2 --threads ${task.cpus} --temp tmp --prefix ${sample_name}
     
-    cp ${sample_name}.results.josn ${ntmprofiler_json}
+    cp ${sample_name}.results.json ${ntmprofiler_json}
 
     cp ${sample_name}_report.json ${sample_name}_report_previous.json
 

workflows/vcfpredict.nf

@@ -11,6 +11,7 @@ include {tbtamr} from '../modules/vcfpredictModules.nf' params(params)
 include {tbtamr_collate} from '../modules/vcfpredictModules.nf' params(params)
 include {tbprofiler_collate} from '../modules/vcfpredictModules.nf' params(params)
 include {ntmprofiler} from '../modules/vcfpredictModules.nf' params(params)
+include {ntmprofiler_collate} from '../modules/vcfpredictModules.nf' params(params)
 // define workflow component
 workflow vcfpredict {