diff --git a/artic.sh b/artic.sh index 83527a0..fcfa887 100644 --- a/artic.sh +++ b/artic.sh @@ -12,7 +12,8 @@ # Needed for conda on our set-up source ~/.bashrc # Prevent Qt plotting issues with unattached X11 display -DISPLAY="" +# No longer needed with artic v.1.2.0+, (uncomment for older versions of artic) +#DISPLAY="" TIME=$(date) HOST=$(hostname) @@ -109,7 +110,7 @@ READS_POST=$(awk '{s++}END{print s/4}' ${TMPDIR}/${RUN_NAME}_${BARCODE}.fastq) PC_PLEX=$(echo "scale=8; (${READS_POST}/${READS_PRE})*100" | bc | xargs printf "%.2f\n") echo "Reads post guppyplex: ${READS_POST} (${PC_PLEX}%)" -# artic minion final stage, many output / temp files written to ${TMPDIR} +# artic minion final stage, many output / temp files written to ${TMPDIR} echo "Running artic minion --normalise ${NORMALISE} on ${CPU} threads, fast5 dir is: ${INPUT_DIR}/fast5_pass" artic minion --normalise ${NORMALISE} --threads ${CPU} --scheme-directory ${SCHEME_DIR} --read-file ${TMPDIR}/${RUN_NAME}_${BARCODE}.fastq --fast5-directory ${INPUT_DIR}/fast5_pass --sequencing-summary ${SEQ_SUM} ${PRIMERS} ${SAMPLE} @@ -198,8 +199,10 @@ echo "Creating output dir at ${OUTPUT_DIR}/processed/${RUN_NAME}" mkdir -p ${OUTPUT_DIR}/processed/${RUN_NAME} echo "Copying ${SAMPLE}.* ..." cp ${TMPDIR}/${SAMPLE}.* ${OUTPUT_DIR}/processed/${RUN_NAME} -echo "Copying ${SAMPLE}-* ..." -cp ${TMPDIR}/${SAMPLE}-* ${OUTPUT_DIR}/processed/${RUN_NAME} +# Needed for older artic v.1.1.3 which produced .pngs with a different output +# convention, commented out now as not produced in v.1.2.0 or higher +#echo "Copying ${SAMPLE}-* ..." +#cp ${TMPDIR}/${SAMPLE}-* ${OUTPUT_DIR}/processed/${RUN_NAME} echo "Gzipping ${RUN_NAME}_${BARCODE}.fastq ..." # Needs pigz, conda install pigz, into your artic-ncov2019 env @@ -220,7 +223,7 @@ conda activate pangolin pangolin -t ${CPU} -o ${TMPDIR}/${SAMPLE}.pangolin --tempdir ${TMPDIR} ${TMPDIR}/${SAMPLE}.consensus.fasta > ${OUTPUT_DIR}/processed/${RUN_NAME}/${SAMPLE}.pangolin.out 2>${OUTPUT_DIR}/processed/${RUN_NAME}/${SAMPLE}.pangolin.err cp ${TMPDIR}/${SAMPLE}.pangolin/lineage_report.csv ${OUTPUT_DIR}/processed/${RUN_NAME}/${SAMPLE}.pangolin.lineage_report.csv echo "Lineage report:" -column -t -s ',' ${TMPDIR}/${SAMPLE}.pangolin/lineage_report.csv +column -t -s ',' ${TMPDIR}/${SAMPLE}.pangolin/lineage_report.csv echo "" # Clean-up temp dir