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pipeline.xml
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pipeline.xml
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<?xml version="1.0" encoding="UTF-8"?>
<pipeline xmlns="http://www.sing-group.org/compi/pipeline-1.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<version>1.12.0</version>
<params>
<param name="working_dir" shortName="w" global="true" defaultValue="/working_dir">Path of the working directory.</param>
<param name="input_dir" shortName="id" global="true" defaultValue="input">Name of the input directory (under working_dir).</param>
<param name="scripts_dir" shortName="sd" global="true" defaultValue="/opt/Fast_Screen/">Path of the directory containing the pipeline scripts.</param>
<flag name="skip_code_ml" shortName="scm" global="true">If this flag is present, then the CodeML execution is skipped.</flag>
<!-- Intermediate results directories -->
<param name="renamed_seqs_dir" shortName="rsd" defaultValue="renamed_seqs">Name of the directory (under working_dir) to place the file with the renamed sequences.</param>
<param name="renamed_seqs_maps_dir" shortName="rsmd" defaultValue="renamed_seqs_mappings">Name of the directory (under working_dir) to place the file with the mappings to produce the renamed sequences.</param>
<param name="aligned_seqs_dir" shortName="asd" defaultValue="ali">Name of the directory (under working_dir) to place the file with the aligned sequences.</param>
<param name="tree_dir" shortName="td" defaultValue="tree">Name of the directory (under working_dir) to place the file with the tree.</param>
<param name="fubar_files_dir" shortName="fd" defaultValue="FUBAR_files">Name of the directory (under working_dir) to place the file with the FUBAR input files.</param>
<param name="fubar_results_dir" shortName="frd" defaultValue="FUBAR_results">Name of the directory (under working_dir) to place the file with the FUBAR results.</param>
<param name="fubar_config_files_dir" shortName="fcd" defaultValue="config_files">Name of the directory (under working_dir) to place the file with the FUBAR configuration.</param>
<param name="codeML_results_dir" shortName="crd" defaultValue="codeML_results">Name of the directory (under working_dir) to place the file with the CodeML results.</param>
<param name="codeML_config_files_dir" shortName="ccfd" defaultValue="config_files">Name of the directory (under working_dir) to place the file with the CodeML configuration files.</param>
</params>
<tasks>
<task id="check-minimum-sequences">
${scripts_dir}/check_minimum_sequences ${working_dir} ${input_dir}
if [ -f ${working_dir}/files_without_minimum_sequences ]; then
echo "There are input files without the minimum number of sequences (4). Check the list of files in files_without_minimum_sequences."
exit 1
fi
</task>
<foreach id="rename-headers" after="check-minimum-sequences"
params="input_dir renamed_seqs_dir renamed_seqs_maps_dir"
of="command" in="ls ${working_dir}/${input_dir}" as="input_fasta">
mkdir -p ${working_dir}/${renamed_seqs_dir}
mkdir -p ${working_dir}/${renamed_seqs_maps_dir}
${scripts_dir}/rename_headers ${input_fasta} ${input_dir} ${renamed_seqs_dir} ${working_dir} ${renamed_seqs_maps_dir}
</foreach>
<foreach id="clustal-omega" after="*rename-headers"
params="renamed_seqs_dir aligned_seqs_dir"
of="command" in="ls ${working_dir}/${input_dir}" as="input_fasta">
mkdir -p ${working_dir}/${aligned_seqs_dir}
${scripts_dir}/run_clustal_omega ${input_fasta} ${renamed_seqs_dir} ${aligned_seqs_dir} ${working_dir}
</foreach>
<foreach id="fastree" after="*clustal-omega"
params="aligned_seqs_dir tree_dir"
of="command" in="ls ${working_dir}/${input_dir}" as="input_fasta">
mkdir -p ${working_dir}/${tree_dir}
${scripts_dir}/run_fasttree ${input_fasta} ${aligned_seqs_dir} ${tree_dir} ${working_dir}
</foreach>
<foreach id="fubar-prepare" after="*fastree"
params="aligned_seqs_dir tree_dir fubar_files_dir"
of="command" in="ls ${working_dir}/${input_dir}" as="input_fasta">
mkdir -p ${working_dir}/${fubar_files_dir}
${scripts_dir}/prepare_FUBAR_files ${input_fasta} ${aligned_seqs_dir} ${tree_dir} ${fubar_files_dir} ${working_dir}
</foreach>
<foreach id="fubar-run" after="*fubar-prepare"
params="fubar_results_dir fubar_files_dir fubar_config_files_dir"
of="command" in="ls ${working_dir}/${input_dir}" as="input_fasta">
mkdir -p ${working_dir}/${fubar_results_dir} ${working_dir}/${fubar_files_dir}/${fubar_config_files_dir}
${scripts_dir}/run_FUBAR ${input_fasta}.fubar ${fubar_files_dir} ${fubar_config_files_dir} ${fubar_results_dir} ${working_dir}
</foreach>
<foreach id="fubar-pss" after="*fubar-run"
params="fubar_results_dir"
of="command" in="ls ${working_dir}/${input_dir}" as="input_fasta">
${scripts_dir}/check_pos_FUBAR ${input_fasta}.fubar ${fubar_results_dir} ${working_dir}
</foreach>
<!-- Run codeML if FUBAR detects no PSS and the skip_code_ml flag is not present. -->
<foreach id="codeml-check-limit" after="*fubar-pss"
if="${scripts_dir}/check_run_codeML ${input_fasta} ${working_dir} ${skip_code_ml}"
params="renamed_seqs_dir input_dir aligned_seqs_dir tree_dir"
of="command" in="ls ${working_dir}/${input_dir}" as="input_fasta">
${scripts_dir}/check_codeML_limit ${input_fasta} ${renamed_seqs_dir} ${input_dir} ${aligned_seqs_dir} ${tree_dir} ${working_dir}
</foreach>
<foreach id="codeml-clustal-omega" after="*codeml-check-limit"
if="${scripts_dir}/check_run_codeML ${input_fasta} ${working_dir} ${skip_code_ml}"
params="renamed_seqs_dir aligned_seqs_dir"
of="command" in="ls ${working_dir}/${input_dir}" as="input_fasta">
${scripts_dir}/run_clustal_omega ${input_fasta} ${renamed_seqs_dir} ${aligned_seqs_dir} ${working_dir}
</foreach>
<foreach id="codeml-fastree" after="*codeml-clustal-omega"
if="${scripts_dir}/check_run_codeML ${input_fasta} ${working_dir} ${skip_code_ml}"
params="aligned_seqs_dir tree_dir"
of="command" in="ls ${working_dir}/${input_dir}" as="input_fasta">
${scripts_dir}/run_fasttree ${input_fasta} ${aligned_seqs_dir} ${tree_dir} ${working_dir}
</foreach>
<foreach id="codeml-prepare" after="*codeml-fastree"
if="${scripts_dir}/check_run_codeML ${input_fasta} ${working_dir} ${skip_code_ml}"
params="input_dir tree_dir"
of="command" in="ls ${working_dir}/${input_dir}" as="input_fasta">
mkdir -p ${working_dir}/${tree_dir}.codeML
${scripts_dir}/prepare_trees_for_codeML ${input_fasta} ${tree_dir} ${working_dir}
</foreach>
<foreach id="codeml-run" after="*codeml-prepare"
if="${scripts_dir}/check_run_codeML ${input_fasta} ${working_dir} ${skip_code_ml}"
params="aligned_seqs_dir codeML_results_dir codeML_config_files_dir tree_dir"
of="command" in="ls ${working_dir}/${input_dir}" as="input_fasta">
mkdir -p ${working_dir}/${codeML_results_dir} ${working_dir}/${codeML_results_dir}/${codeML_config_files_dir}
${scripts_dir}/run_codeML ${input_fasta} 2 ${codeML_results_dir} ${codeML_config_files_dir} ${aligned_seqs_dir} ${tree_dir} ${working_dir}
</foreach>
<foreach id="codeml-pss" after="*codeml-run"
if="${scripts_dir}/check_run_codeML ${input_fasta} ${working_dir} ${skip_code_ml}"
params="aligned_seqs_dir codeML_results_dir codeML_config_files_dir tree_dir"
of="command" in="ls ${working_dir}/${input_dir}" as="input_fasta">
${scripts_dir}/check_pos_codeML ${input_fasta} ${codeML_results_dir} ${working_dir}
</foreach>
<task id="collect-short-lists" after="codeml-pss">
touch ${working_dir}/FUBAR_short_list ${working_dir}/codeML_short_list
cat ${working_dir}/FUBAR_short_list ${working_dir}/codeML_short_list > ${working_dir}/short_list.tmp
sort ${working_dir}/short_list.tmp > ${working_dir}/short_list
rm ${working_dir}/short_list.tmp
</task>
</tasks>
<metadata>
<task-description id="check-minimum-sequences">Checks that all input files have the minimum number of sequences (4). If so, such files are reported in the files_without_minimum_sequences and the pipeline execution is stopped.</task-description>
<task-description id="rename-headers">Renames the sequence headers.</task-description>
<task-description id="clustal-omega">Aligns sequences using ClustalOmega.</task-description>
<task-description id="fastree">Generates a phylogenetic tree using FastTree.</task-description>
<task-description id="fubar-prepare">Prepares input files for FUBAR.</task-description>
<task-description id="fubar-pss">Processes the FUBAR results.</task-description>
<task-description id="fubar-run">Looks for PSS with FUBAR.</task-description>
<task-description id="codeml-check-limit">Checks the codeML limits.</task-description>
<task-description id="codeml-clustal-omega">Aligns sequences using ClustalOmega for codeML run.</task-description>
<task-description id="codeml-fastree">Generates a phylogenetic tree using FastTree for codeML run.</task-description>
<task-description id="codeml-prepare">Prepares input files for codeML.</task-description>
<task-description id="codeml-run">Looks for PSS with FUBAR..</task-description>
<task-description id="codeml-pss">Processes the codeML results.</task-description>
<task-description id="collect-short-lists">Collects the FUBAR and codeML results into the short list files.</task-description>
</metadata>
</pipeline>