Move BUSCO bash code a script

CHANGELOG.md

@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#429](https://github.com/nf-core/mag/pull/429) - Replaced hardcoded CheckM database auto-download URL to a parameter (reported by @erikrikarddaniel, fix by @jfy133)
 - [#441](https://github.com/nf-core/mag/pull/441) - Deactivated CONCOCT in AWS 'full test' due to very long runtime (fix by @jfy133).
 - [#442](https://github.com/nf-core/mag/pull/442) - Remove warning when BUSCO finds no genes in bins, as this can be expected in some datasets (reported by @Lumimar, fix by @jfy133).
+- [#444](https://github.com/nf-core/mag/pull/444) - Moved BUSCO bash code to script (by @jfy133)
 
 ### `Fixed`
 

bin/run_busco.sh

@@ -0,0 +1,155 @@
+#! /usr/bin/env bash
+
+p=$1
+cp_augustus_config=$2
+db=$3
+bin=$4
+task_cpus=$5
+lineage_dataset_provided=$6
+busco_clean=$7
+
+# ensure augustus has write access to config directory
+if [ ${cp_augustus_config} = "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 [ ${lineage_dataset_provided} = "Y" ]; then
+    mkdir dataset
+    mv ${db} 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 ${p} \
+    --mode genome \
+    --in ${bin} \
+    --cpu ${task_cpus} \
+    --out "BUSCO" >${bin}_busco.log 2>${bin}_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 [ ${lineage_dataset_provided} = "Y" ]; then
+        cp BUSCO/short_summary.specific.${db_name_spec}.BUSCO.txt short_summary.specific_lineage.${db_name_spec}.${bin}.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:\tBUSCO did not find any match.' ${bin}_busco.log; then
+            echo "WARNING: BUSCO could not find any genes for the provided lineage dataset! See also ${bin}_busco.log."
+            echo -e "${bin}\tNo genes" >"${bin}_busco.failed_bin.txt"
+        fi
+    else
+        # auto lineage selection
+        if { egrep -q $'INFO:\t\\S+ selected' ${bin}_busco.log &&
+            egrep -q $'INFO:\tLineage \\S+ is selected, supported by ' ${bin}_busco.log; } ||
+            { egrep -q $'INFO:\t\\S+ selected' ${bin}_busco.log &&
+                egrep -q $'INFO:\tThe results from the Prodigal gene predictor indicate that your data belongs to the mollicutes clade. Testing subclades...' ${bin}_busco.log &&
+                egrep -q $'INFO:\tUsing local lineages directory ' ${bin}_busco.log; }; then
+            # the second statement is necessary, because certain mollicute clades use a different genetic code, are not part of the BUSCO placement tree, are tested separately
+            # and cause different log messages
+            echo "Domain and specific lineage could be selected by BUSCO."
+            cp BUSCO/short_summary.specific.${db_name_spec}.BUSCO.txt short_summary.specific_lineage.${db_name_spec}.${bin}.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.${db_name_spec}.${bin}.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.${db_name_gen}.${bin}.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 >${bin}_buscos.${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 >${bin}_buscos.${db_name_gen}.fna.gz
+                break
+            done
+
+        elif egrep -q $'INFO:\t\\S+ selected' ${bin}_busco.log && egrep -q $'INFO:\tNo marker genes were found. Root lineage \\S+ is kept' ${bin}_busco.log; then
+            echo "Domain could be selected by BUSCO, but no more specific lineage."
+            cp BUSCO/short_summary.specific.${db_name_spec}.BUSCO.txt short_summary.domain.${db_name_spec}.${bin}.txt
+
+        elif egrep -q $'INFO:\t\\S+ selected' ${bin}_busco.log && egrep -q $'INFO:\tNot enough markers were placed on the tree \\([0-9]*\\). Root lineage \\S+ is kept' ${bin}_busco.log; then
+            echo "Domain could be selected by BUSCO, but no more specific lineage."
+            cp BUSCO/short_summary.specific.${db_name_spec}.BUSCO.txt short_summary.domain.${db_name_spec}.${bin}.txt
+
+        elif egrep -q $'INFO:\t\\S+ selected' ${bin}_busco.log && egrep -q $'INFO:\tRunning virus detection pipeline' ${bin}_busco.log; then
+            # TODO double-check if selected dataset is not one of bacteria_*, archaea_*, eukaryota_*?
+            echo "Domain could not be selected by BUSCO, but virus dataset was selected."
+            cp BUSCO/short_summary.specific.${db_name_spec}.BUSCO.txt short_summary.specific_lineage.${db_name_spec}.${bin}.txt
+        else
+            echo "ERROR: Some not expected case occurred! See ${bin}_busco.log." >&2
+            exit 1
+        fi
+    fi
+
+    for f in BUSCO/run_${db_name_spec}/busco_sequences/single_copy_busco_sequences/*faa; do
+        cat BUSCO/run_${db_name_spec}/busco_sequences/single_copy_busco_sequences/*faa | gzip >${bin}_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_${db_name_spec}/busco_sequences/single_copy_busco_sequences/*fna | gzip >${bin}_buscos.${db_name_spec}.fna.gz
+        break
+    done
+
+elif egrep -q $'ERROR:\tNo genes were recognized by BUSCO' ${bin}_busco.err; then
+    echo "WARNING: BUSCO analysis failed due to no recognized genes! See also ${bin}_busco.err."
+    echo -e "${bin}\tNo genes" >"${bin}_busco.failed_bin.txt"
+
+elif egrep -q $'INFO:\t\\S+ selected' ${bin}_busco.log && egrep -q $'ERROR:\tPlacements failed' ${bin}_busco.err; then
+    echo "WARNING: BUSCO analysis failed due to failed placements! See also ${bin}_busco.err. Still using results for selected generic lineage dataset."
+    echo -e "${bin}\tPlacements failed" >"${bin}_busco.failed_bin.txt"
+
+    message=$(egrep $'INFO:\t\\S+ selected' ${bin}_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.${db_name_gen}.${bin}.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 >${bin}_buscos.${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 >${bin}_buscos.${db_name_gen}.fna.gz
+        break
+    done
+
+else
+    echo "ERROR: BUSCO analysis failed for some unknown reason! See also ${bin}_busco.err." >&2
+    exit 1
+fi
+
+# additionally output genes predicted with Prodigal (GFF3)
+if [ -f BUSCO/logs/prodigal_out.log ]; then
+    mv BUSCO/logs/prodigal_out.log "${bin}_prodigal.gff"
+fi
+
+# if needed delete temporary BUSCO files
+if [ ${busco_clean} = "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

modules/local/busco.nf

@@ -38,151 +38,7 @@ process BUSCO {
             p += " --offline --download_path ${download_folder}"
     }
     """
-    # ensure augustus has write access to config directory
-    if [ ${cp_augustus_config} = "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 [ ${lineage_dataset_provided} = "Y" ] ; then
-        mkdir dataset
-        mv ${db} 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 ${p} \
-        --mode genome \
-        --in ${bin} \
-        --cpu "${task.cpus}" \
-        --out "BUSCO" > ${bin}_busco.log 2> ${bin}_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 [ ${lineage_dataset_provided} = "Y" ]; then
-            cp BUSCO/short_summary.specific.\${db_name_spec}.BUSCO.txt short_summary.specific_lineage.\${db_name_spec}.${bin}.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:\tBUSCO did not find any match.' ${bin}_busco.log ; then
-                echo "WARNING: BUSCO could not find any genes for the provided lineage dataset! See also ${bin}_busco.log."
-                echo -e "${bin}\tNo genes" > "${bin}_busco.failed_bin.txt"
-            fi
-        else
-            # auto lineage selection
-            if { egrep -q \$'INFO:\t\\S+ selected' ${bin}_busco.log \
-                && egrep -q \$'INFO:\tLineage \\S+ is selected, supported by ' ${bin}_busco.log ; } || \
-                { egrep -q \$'INFO:\t\\S+ selected' ${bin}_busco.log \
-                && egrep -q \$'INFO:\tThe results from the Prodigal gene predictor indicate that your data belongs to the mollicutes clade. Testing subclades...' ${bin}_busco.log \
-                && egrep -q \$'INFO:\tUsing local lineages directory ' ${bin}_busco.log ; }; then
-                # the second statement is necessary, because certain mollicute clades use a different genetic code, are not part of the BUSCO placement tree, are tested separately
-                # and cause different log messages
-                echo "Domain and specific lineage could be selected by BUSCO."
-                cp BUSCO/short_summary.specific.\${db_name_spec}.BUSCO.txt short_summary.specific_lineage.\${db_name_spec}.${bin}.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}.${bin}.txt
-                    db_name_gen=\${db_name_spec}
-                else
-                    [[ \$summaries_gen =~ BUSCO/short_summary.generic.(.*).BUSCO.txt ]];
-                    db_name_gen="\${BASH_REMATCH[1]}"
-                    echo "Used generic lineage dataset: \${db_name_gen}"
-                    cp BUSCO/short_summary.generic.\${db_name_gen}.BUSCO.txt short_summary.domain.\${db_name_gen}.${bin}.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 >${bin}_buscos.\${db_name_gen}.faa.gz
-                    break
-                done
-                for f in BUSCO/run_\${db_name_gen}/busco_sequences/single_copy_busco_sequences/*fna; do
-                    cat BUSCO/run_\${db_name_gen}/busco_sequences/single_copy_busco_sequences/*fna | gzip >${bin}_buscos.\${db_name_gen}.fna.gz
-                    break
-                done
-
-            elif egrep -q \$'INFO:\t\\S+ selected' ${bin}_busco.log && egrep -q \$'INFO:\tNo marker genes were found. Root lineage \\S+ is kept' ${bin}_busco.log ; then
-                echo "Domain could be selected by BUSCO, but no more specific lineage."
-                cp BUSCO/short_summary.specific.\${db_name_spec}.BUSCO.txt short_summary.domain.\${db_name_spec}.${bin}.txt
-
-            elif egrep -q \$'INFO:\t\\S+ selected' ${bin}_busco.log && egrep -q \$'INFO:\tNot enough markers were placed on the tree \\([0-9]*\\). Root lineage \\S+ is kept' ${bin}_busco.log ; then
-                echo "Domain could be selected by BUSCO, but no more specific lineage."
-                cp BUSCO/short_summary.specific.\${db_name_spec}.BUSCO.txt short_summary.domain.\${db_name_spec}.${bin}.txt
-
-            elif egrep -q \$'INFO:\t\\S+ selected' ${bin}_busco.log && egrep -q \$'INFO:\tRunning virus detection pipeline' ${bin}_busco.log ; then
-                # TODO double-check if selected dataset is not one of bacteria_*, archaea_*, eukaryota_*?
-                echo "Domain could not be selected by BUSCO, but virus dataset was selected."
-                cp BUSCO/short_summary.specific.\${db_name_spec}.BUSCO.txt short_summary.specific_lineage.\${db_name_spec}.${bin}.txt
-            else
-                echo "ERROR: Some not expected case occurred! See ${bin}_busco.log." >&2
-                exit 1
-            fi
-        fi
-
-        for f in BUSCO/run_\${db_name_spec}/busco_sequences/single_copy_busco_sequences/*faa; do
-            cat BUSCO/run_\${db_name_spec}/busco_sequences/single_copy_busco_sequences/*faa | gzip >${bin}_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 >${bin}_buscos.\${db_name_spec}.fna.gz
-            break
-        done
-
-    elif egrep -q \$'ERROR:\tNo genes were recognized by BUSCO' ${bin}_busco.err ; then
-        echo "WARNING: BUSCO analysis failed due to no recognized genes! See also ${bin}_busco.err."
-        echo -e "${bin}\tNo genes" > "${bin}_busco.failed_bin.txt"
-
-    elif egrep -q \$'INFO:\t\\S+ selected' ${bin}_busco.log && egrep -q \$'ERROR:\tPlacements failed' ${bin}_busco.err ; then
-        echo "WARNING: BUSCO analysis failed due to failed placements! See also ${bin}_busco.err. Still using results for selected generic lineage dataset."
-        echo -e "${bin}\tPlacements failed" > "${bin}_busco.failed_bin.txt"
-
-        message=\$(egrep \$'INFO:\t\\S+ selected' ${bin}_busco.log)
-        [[ \$message =~ INFO:[[:space:]]([_[:alnum:]]+)[[:space:]]selected ]];
-        db_name_gen="\${BASH_REMATCH[1]}"
-        most_spec_db=\${db_name_gen}
-        echo "Used generic lineage dataset: \${db_name_gen}"
-        cp BUSCO/auto_lineage/run_\${db_name_gen}/short_summary.txt short_summary.domain.\${db_name_gen}.${bin}.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 >${bin}_buscos.\${db_name_gen}.faa.gz
-            break
-        done
-        for f in BUSCO/auto_lineage/run_\${db_name_gen}/busco_sequences/single_copy_busco_sequences/*fna; do
-            cat BUSCO/auto_lineage/run_\${db_name_gen}/busco_sequences/single_copy_busco_sequences/*fna | gzip >${bin}_buscos.\${db_name_gen}.fna.gz
-            break
-        done
-
-    else
-        echo "ERROR: BUSCO analysis failed for some unknown reason! See also ${bin}_busco.err." >&2
-        exit 1
-    fi
-
-    # additionally output genes predicted with Prodigal (GFF3)
-    if [ -f BUSCO/logs/prodigal_out.log ]; then
-        mv BUSCO/logs/prodigal_out.log "${bin}_prodigal.gff"
-    fi
-
-    # if needed delete temporary BUSCO files
-    if [ ${busco_clean} = "Y" ]; then
-        find . -depth -type d -name "augustus_config" -execdir rm -rf "{}" \\;
-        find . -depth -type d -name "auto_lineage" -execdir rm -rf "{}" \\;
-        find . -depth -type d -name "run_*" -execdir rm -rf "{}" +
-    fi
+    run_busco.sh "${p}" "${cp_augustus_config}" "${db}" "${bin}" ${task.cpus} "${lineage_dataset_provided}" "${busco_clean}"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":