--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.3.0/modules/centrifuge/extract/main.nf	Tue Jul 19 10:07:24 2022 -0400
@@ -0,0 +1,59 @@
+process CENTRIFUGE_EXTRACT {
+    tag "$meta.id"
+    label 'process_low'
+
+    //seqkit container contains required bash and other utilities
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
+    conda (params.enable_conda ? "conda-forge::sed=4.7 conda-forge::coreutils" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-039542721b6b463b663872ba8b7e9fbc05f01925:1de88053ebf8fb9884758395c4871f642c57750c-0':
+        'quay.io/biocontainers/mulled-v2-039542721b6b463b663872ba8b7e9fbc05f01925:1de88053ebf8fb9884758395c4871f642c57750c-0' }"
+
+    input:
+    tuple val(meta), path(centrifuge_report)
+    tuple val(meta), path(centrifuge_output)
+
+    output:
+    tuple val(meta), path('*.extract-centrifuge-bug-ids.txt'), emit: extracted
+    path "versions.yml"                                      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    grep -F '${params.centrifuge_extract_bug}' $centrifuge_report \
+        | cut -f2 \
+        | sort -u \
+        | while read -r taxId; do
+            echo -e "\t\$taxId"'\$'
+        done > gotcha.txt
+
+    cut -f1-3 $centrifuge_output | grep -E -f gotcha.txt | cut -f1 | sort -u > ${prefix}.extract-centrifuge-bug-ids.txt || true
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
+    END_VERSIONS
+
+    ver=""
+    sedver=""
+
+    if [ "${workflow.containerEngine}" != "null" ]; then
+        ver=\$( cut --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
+        sedver="\$ver"
+    else
+        ver=\$( cut --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
+        sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
+    fi
+
+    cat <<-END_VERSIONS >> versions.yml
+        cut: \$ver
+        tail: \$ver
+        sort: \$ver
+        sed: \$sedver
+    END_VERSIONS
+    """
+}
\ No newline at end of file