Move BUSCO.nf process to a bash script

[jfy133]

Description of feature

As this makes ugly warning messages when running -with-tower

I'm shamefully tagging @skrakau to look into this as the bash script scares me too much to try doing it myself 😅 (sorry!)

WARN: Tower request field `tasks.script` exceeds expected size | offending value: `
    # ensure augustus has write access to config directory
    if [ Y = "Y" ] ; then
        cp -r /usr/local/config/ augustus_config/
        export AUGUSTUS_CONFIG_PATH=augustus_config
    fi

    # place db in extra folder to ensure BUSCO recognizes it as path (instead of downloading it)
    if [ Y = "Y" ] ; then
        mkdir dataset
        mv bacteria_odb10 dataset/
    fi

    # set nullgob: if pattern matches no files, expand to a null string rather than to itself
    shopt -s nullglob

    # only used for saving busco downloads
    most_spec_db="NA"

    if busco --lineage_dataset dataset/bacteria_odb10         --mode genome         --in MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa         --cpu "2"         --out "BUSCO" > MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log 2> MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.err; then

        # get name of used specific lineage dataset
        summaries=(BUSCO/short_summary.specific.*.BUSCO.txt)
        if [ ${#summaries[@]} -ne 1 ]; then
            echo "ERROR: none or multiple 'BUSCO/short_summary.specific.*.BUSCO.txt' files found. Expected one."
            exit 1
        fi
        [[ $summaries =~ BUSCO/short_summary.specific.(.*).BUSCO.txt ]];
        db_name_spec="${BASH_REMATCH[1]}"
        most_spec_db=${db_name_spec}
        echo "Used specific lineage dataset: ${db_name_spec}"

        if [ Y = "Y" ]; then
            cp BUSCO/short_summary.specific.${db_name_spec}.BUSCO.txt short_summary.specific_lineage.${db_name_spec}.MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa.txt

            # if lineage dataset is provided, BUSCO analysis does not fail in case no genes can be found as when using the auto selection setting
            # report bin as failed to allow consistent warnings within the pipeline for both settings
            if egrep -q $'WARNING:      BUSCO did not find any match.' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log ; then
                echo "WARNING: BUSCO could not find any genes for the provided lineage dataset! See also MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log."
                echo -e "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa    No genes" > "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.failed_bin.txt"
            fi
        else
            # auto lineage selection
            if { egrep -q $'INFO:       \S+ selected' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log                 && egrep -q $'INFO: Lineage \S+ is selected, supported by ' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log ; } ||                 { egrep -q $'INFO: \S+ selected' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log                 && egrep -q $'INFO: The results from the Prodigal gene predictor indicate that your data belongs to the mollicutes clade. Testing subclades...' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log                 && egrep -q $'INFO:   Using local lineages directory ' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log ; }; then
                # the second statement is necessary, because certain mollicute clades use a different genetic code, are not part of the BUSCO placement tree, are tested separately
                # and cause different log messages
                echo "Domain and specific lineage could be selected by BUSCO."
                cp BUSCO/short_summary.specific.${db_name_spec}.BUSCO.txt short_summary.specific_lineage.${db_name_spec}.MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa.txt

                db_name_gen=""
                summaries_gen=(BUSCO/short_summary.generic.*.BUSCO.txt)
                if [ ${#summaries_gen[@]} -lt 1 ]; then
                    echo "No 'BUSCO/short_summary.generic.*.BUSCO.txt' file found. Assuming selected domain and specific lineages are the same."
                    cp BUSCO/short_summary.specific.${db_name_spec}.BUSCO.txt short_summary.domain.${db_name_spec}.MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa.txt
                    db_name_gen=${db_name_spec}
                else
                    [[ $summaries_gen =~ BUSCO/short_summary.generic.(.*).BUSCO.txt ]];
                    db_name_gen="${BASH_REMATCH[1]}"
                    echo "Used generic lineage dataset: ${db_name_gen}"
                    cp BUSCO/short_summary.generic.${db_name_gen}.BUSCO.txt short_summary.domain.${db_name_gen}.MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa.txt
                fi

                for f in BUSCO/run_${db_name_gen}/busco_sequences/single_copy_busco_sequences/*faa; do
                    cat BUSCO/run_${db_name_gen}/busco_sequences/single_copy_busco_sequences/*faa | gzip >MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_buscos.${db_name_gen}.faa.gz
                    break
                done
                for f in BUSCO/run_${db_name_gen}/busco_sequences/single_copy_busco_sequences/*fna; do
                    cat BUSCO/run_${db_name_gen}/busco_sequences/single_copy_busco_sequences/*fna | gzip >MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_buscos.${db_name_gen}.fna.gz
                    break
                done

            elif egrep -q $'INFO:       \S+ selected' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log && egrep -q $'INFO: No marker genes were found. Root lineage \S+ is kept' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log ; then
                echo "Domain could be selected by BUSCO, but no more specific lineage."
                cp BUSCO/short_summary.specific.${db_name_spec}.BUSCO.txt short_summary.domain.${db_name_spec}.MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa.txt

            elif egrep -q $'INFO:       \S+ selected' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log && egrep -q $'INFO: Not enough markers were placed on the tree \([0-9]*\). Root lineage \S+ is kept' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log ; then
                echo "Domain could be selected by BUSCO, but no more specific lineage."
                cp BUSCO/short_summary.specific.${db_name_spec}.BUSCO.txt short_summary.domain.${db_name_spec}.MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa.txt

            elif egrep -q $'INFO:       \S+ selected' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log && egrep -q $'INFO: Running virus detection pipeline' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log ; then
                # TODO double-check if selected dataset is not one of bacteria_*, archaea_*, eukaryota_*?
                echo "Domain could not be selected by BUSCO, but virus dataset was selected."
                cp BUSCO/short_summary.specific.${db_name_spec}.BUSCO.txt short_summary.specific_lineage.${db_name_spec}.MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa.txt
            else
                echo "ERROR: Some not expected case occurred! See MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log." >&2
                exit 1
            fi
        fi

        for f in BUSCO/run_${db_name_spec}/busco_sequences/single_copy_busco_sequences/*faa; do
            cat BUSCO/run_${db_name_spec}/busco_sequences/single_copy_busco_sequences/*faa | gzip >MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_buscos.${db_name_spec}.faa.gz
            break
        done
        for f in BUSCO/run_${db_name_spec}/busco_sequences/single_copy_busco_sequences/*fna; do
            cat BUSCO/run_${db_name_spec}/busco_sequences/single_copy_busco_sequences/*fna | gzip >MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_buscos.${db_name_spec}.fna.gz
            break
        done

    elif egrep -q $'ERROR:      No genes were recognized by BUSCO' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.err ; then
        echo "WARNING: BUSCO analysis failed due to no recognized genes! See also MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.err."
        echo -e "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa    No genes" > "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.failed_bin.txt"

    elif egrep -q $'INFO:       \S+ selected' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log && egrep -q $'ERROR:        Placements failed' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.err ; then
        echo "WARNING: BUSCO analysis failed due to failed placements! See also MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.err. Still using results for selected generic lineage dataset."
        echo -e "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa    Placements failed" > "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.failed_bin.txt"

        message=$(egrep $'INFO: \S+ selected' MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.log)
        [[ $message =~ INFO:[[:space:]]([_[:alnum:]]+)[[:space:]]selected ]];
        db_name_gen="${BASH_REMATCH[1]}"
        most_spec_db=${db_name_gen}
        echo "Used generic lineage dataset: ${db_name_gen}"
        cp BUSCO/auto_lineage/run_${db_name_gen}/short_summary.txt short_summary.domain.${db_name_gen}.MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa.txt

        for f in BUSCO/auto_lineage/run_${db_name_gen}/busco_sequences/single_copy_busco_sequences/*faa; do
            cat BUSCO/auto_lineage/run_${db_name_gen}/busco_sequences/single_copy_busco_sequences/*faa | gzip >MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_buscos.${db_name_gen}.faa.gz
            break
        done
        for f in BUSCO/auto_lineage/run_${db_name_gen}/busco_sequences/single_copy_busco_sequences/*fna; do
            cat BUSCO/auto_lineage/run_${db_name_gen}/busco_sequences/single_copy_busco_sequences/*fna | gzip >MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_buscos.${db_name_gen}.fna.gz
            break
        done

    else
        echo "ERROR: BUSCO analysis failed for some unknown reason! See also MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_busco.err." >&2
        exit 1
    fi

    # additionally output genes predicted with Prodigal (GFF3)
    if [ -f BUSCO/logs/prodigal_out.log ]; then
        mv BUSCO/logs/prodigal_out.log "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa_prodigal.gff"
    fi

    # if needed delete temporary BUSCO files
    if [ Y ]; then
        find . -depth -type d -name "augustus_config" -execdir rm -rf "{}" \;
        find . -depth -type d -name "auto_lineage" -execdir rm -rf "{}" \;
        find . -depth -type d -name "run_*" -execdir rm -rf "{}" +
    fi

    cat <<-END_VERSIONS > versions.yml
    "NFCORE_MAG:MAG:BUSCO_QC:BUSCO":
        python: $(python --version 2>&1 | sed 's/Python //g')
        R: $(R --version 2>&1 | sed -n 1p | sed 's/R version //' | sed 's/ (.*//')
        busco: $(busco --version 2>&1 | sed 's/BUSCO //g')
    END_VERSIONS
    `, size: 10488 (max: 10240)
    ```