change paths of python, add bin to docker containers

Pathogen-Genomics-Cymru · Oct 25, 2023 · 97276e9 · 97276e9
1 parent 60ad35f
commit 97276e9
Show file tree

Hide file tree

Showing 8 changed files with 24 additions and 14 deletions.
diff --git a/docker/Dockerfile.clockwork-0.9.7 b/docker/Dockerfile.clockwork-0.9.7
@@ -22,6 +22,9 @@ clockwork_version=2364dec4cbf25c844575e19e8fe0a319d10721b5
 ENV PACKAGES="procps curl git build-essential wget zlib1g-dev pkg-config jq r-base-core rsync autoconf libncurses-dev libbz2-dev liblzma-dev libcurl4-openssl-dev cmake tabix libvcflib-tools libssl-dev software-properties-common perl locales locales-all" \
 PYTHON="python2.7 python-dev"
 
+COPY bin/ /opt/bin/
+ENV PATH=/opt/bin:$PATH
+
 RUN apt-get update \
 && apt-get install -y $PACKAGES $PYTHON \
 && curl -fsSL https://www.python.org/ftp/python/${python_version}/Python-${python_version}.tgz | tar -xz \

diff --git a/docker/Dockerfile.preprocessing-0.9.7 b/docker/Dockerfile.preprocessing-0.9.7
@@ -28,6 +28,9 @@ LD_LIBRARY_PATH=/usr/local/lib
 
 RUN export DEBIAN_FRONTEND="noninteractive"
 
+COPY bin/ /opt/bin/
+ENV PATH=/opt/bin:$PATH
+
 RUN apt-get update \
 && DEBIAN_FRONTEND="noninteractive" apt-get install -y $PACKAGES $PYTHON \
 && pip3 install --upgrade pip \

diff --git a/docker/Dockerfile.vcfpredict-0.9.7 b/docker/Dockerfile.vcfpredict-0.9.7
@@ -13,6 +13,9 @@ piezo_version=0.3 \
 gnomonicus_version=1.1.2 \
 tuberculosis_amr_catalogues=12d38733ad2e238729a3de9f725081e1d4872968
 
+COPY bin/ /opt/bin/
+ENV PATH=/opt/bin:$PATH
+
 RUN apt-get update \
 && DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata \
 && apt-get install -y $PACKAGES $PYTHON \

diff --git a/modules/clockworkModules.nf b/modules/clockworkModules.nf
@@ -46,8 +46,8 @@ process alignToRef {
     samtools index ${bam} ${bai}
     samtools stats ${bam} > ${stats}
 
-    python3 ${baseDir}/bin/parse_samtools_stats.py ${bam} ${stats} > ${stats_json}
-    python3 ${baseDir}/bin/create_final_json.py ${stats_json} ${species_json}
+    parse_samtools_stats.py ${bam} ${stats} > ${stats_json}
+    create_final_json.py ${stats_json} ${species_json}
 
     cp ${sample_name}_report.json ${sample_name}_report_previous.json
 

diff --git a/modules/getversionModules.nf b/modules/getversionModules.nf
@@ -12,7 +12,7 @@ process getversion {
     script:
 
     """
-    python3 ${baseDir}/bin/software-json.py ${params.sing_dir} ${params.config_dir}
+    software-json.py ${params.sing_dir} ${params.config_dir}
     """
 
     stub:

diff --git a/modules/preprocessingModules.nf b/modules/preprocessingModules.nf
@@ -296,9 +296,9 @@ process kraken2 {
     """
     kraken2 --threads ${task.cpus} --db . --output ${kraken2_read_classification} --report ${kraken2_report} --paired $fq1 $fq2
     
-    python3  ${baseDir}/bin/parse_kraken_report2.py ${kraken2_report} ${kraken2_json} 0.5 5000
+    parse_kraken_report2.py ${kraken2_report} ${kraken2_json} 0.5 5000
 
-    ${baseDir}/bin/extract_kraken_reads.py -k ${kraken2_read_classification} -r ${kraken2_report} -s $fq1 -s2 $fq2 -o ${nonBac_depleted_reads_1} -o2 ${nonBac_depleted_reads_2} --taxid 2 --include-children --fastq-output >/dev/null
+    extract_kraken_reads.py -k ${kraken2_read_classification} -r ${kraken2_report} -s $fq1 -s2 $fq2 -o ${nonBac_depleted_reads_1} -o2 ${nonBac_depleted_reads_2} --taxid 2 --include-children --fastq-output >/dev/null
 
     gzip -f ${nonBac_depleted_reads_1}
     gzip -f ${nonBac_depleted_reads_2}
@@ -362,13 +362,13 @@ process afanc {
     if [[ ${run_afanc} =~ /${sample_name}/ ]]
     then
 	afanc screen ${afanc_myco_db} ${fq1} ${fq2} -p 5.0 -n 1000 -o ${sample_name} -t ${task.cpus} -v ${afanc_myco_db}/lineage_profiles/TB_variants.tsv
-	python3 ${baseDir}/bin/reformat_afanc_json.py ${sample_name}/${sample_name}.json
+	reformat_afanc_json.py ${sample_name}/${sample_name}.json
 	printf ${sample_name}
     else
 	afanc screen ${afanc_myco_db} ${fq1} ${fq2} -p 2.0 -n 500 -o ${sample_name} -t ${task.cpus} -v ${afanc_myco_db}/lineage_profiles/TB_variants.tsv
-	python3 ${baseDir}/bin/reformat_afanc_json.py ${sample_name}/${sample_name}.json
+	reformat_afanc_json.py ${sample_name}/${sample_name}.json
 
-	python3 ${baseDir}/bin/identify_tophit_and_contaminants2.py ${afanc_report} ${kraken_json} ${baseDir}/resources/assembly_summary_refseq.txt ${params.species} ${params.unmix_myco} ${baseDir}/resources null
+	identify_tophit_and_contaminants2.py ${afanc_report} ${kraken_json} ${baseDir}/resources/assembly_summary_refseq.txt ${params.species} ${params.unmix_myco} ${baseDir}/resources null
 
 	echo '{"error":"Kraken's top family hit either wasn't Mycobacteriaceae, or there were < 100k Mycobacteriaceae reads. Sample will not proceed further than afanc."}' | jq '.' > ${error_log} && printf "no" && jq -s ".[0] * .[1] * .[2]" ${software_json} ${error_log} ${sample_name}_species_in_sample.json > ${report_json}
 
@@ -504,7 +504,7 @@ process identifyBacterialContaminants {
     report_json = "${sample_name}_report.json"
 
     """
-    python3 ${baseDir}/bin/identify_tophit_and_contaminants2.py ${afanc_json} ${kraken_json} ${baseDir}/resources/assembly_summary_refseq.txt ${params.species} ${params.unmix_myco} ${baseDir}/resources null
+    identify_tophit_and_contaminants2.py ${afanc_json} ${kraken_json} ${baseDir}/resources/assembly_summary_refseq.txt ${params.species} ${params.unmix_myco} ${baseDir}/resources null
 
     contam_to_remove=\$(jq -r '.summary_questions.are_there_contaminants' ${sample_name}_species_in_sample.json)
     acceptable_species=\$(jq -r '.summary_questions.is_the_top_species_appropriate' ${sample_name}_species_in_sample.json)
@@ -663,7 +663,7 @@ process reKraken {
     """
     kraken2 --threads ${task.cpus} --db . --output ${kraken2_read_classification} --report ${kraken2_report} --paired $fq1 $fq2
 
-    python3 ${baseDir}/bin/parse_kraken_report2.py ${kraken2_report} ${kraken2_json} 0.5 5000
+    parse_kraken_report2.py ${kraken2_report} ${kraken2_json} 0.5 5000
     rm -rf ${sample_name}_read_classifications.txt
     """
 
@@ -705,7 +705,7 @@ process reAfanc {
 
     """
     afanc screen ${afanc_myco_db} ${fq1} ${fq2} -p 5.0 -n 1000 -o ${sample_name} -t ${task.cpus} -v ${afanc_myco_db}/lineage_profiles/TB_variants.tsv
-    python3 ${baseDir}/bin/reformat_afanc_json.py ${sample_name}/${sample_name}.json
+    reformat_afanc_json.py ${sample_name}/${sample_name}.json
     printf ${sample_name}
     """
 
@@ -777,7 +777,7 @@ process summarise {
     report_json = "${sample_name}_report.json"
 
     """
-    python3 ${baseDir}/bin/identify_tophit_and_contaminants2.py ${afanc_json} ${kraken_json} ${baseDir}/resources/assembly_summary_refseq.txt ${params.species} ${params.unmix_myco} ${baseDir}/resources ${prev_species_json}
+    identify_tophit_and_contaminants2.py ${afanc_json} ${kraken_json} ${baseDir}/resources/assembly_summary_refseq.txt ${params.species} ${params.unmix_myco} ${baseDir}/resources ${prev_species_json}
 
     contam_to_remove=\$(jq -r '.summary_questions.are_there_contaminants' ${sample_name}_species_in_sample.json)
     acceptable_species=\$(jq -r '.summary_questions.is_the_top_species_appropriate' ${sample_name}_species_in_sample.json)

diff --git a/modules/vcfpredictModules.nf b/modules/vcfpredictModules.nf
@@ -27,7 +27,7 @@ process vcfmix {
     error_log = "${sample_name}_err.json"
 
     """
-    python3 ${baseDir}/bin/run-vcfmix.py ${bcftools_vcf}
+    run-vcfmix.py ${bcftools_vcf}
 
     cp ${sample_name}_report.json ${sample_name}_report_previous.json
 

diff --git a/nextflow.config b/nextflow.config
@@ -74,7 +74,8 @@ profiles {
       }
 
       withLabel:getversion{
-       executor = "local" 
+       executor = "local"
+
       }
 
       withName:downloadContamGenomes {
-Original file line number
+Diff line change
@@ Expand Up / @@ -12,7 +12,7 @@ process getversion { @@
         script:
         """
-        python3 ${baseDir}/bin/software-json.py ${params.sing_dir} ${params.config_dir}
+        software-json.py ${params.sing_dir} ${params.config_dir}
         """
         stub:
@@ Expand Down @@