pipeline.xml

<?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>1.2.4</version>

	<params>
		<param name="host_working_dir" shortName="hw" global="true">Path of the working directory in the host.</param>
		<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">Path of the directory containing the input FASTA files.</param>
		<param name="scripts_dir" shortName="sd" global="true" defaultValue="/opt/scripts/">Path of the directory containing the pipeline scripts.</param>
		
		<param name="sequence_limit" shortName="sl" defaultValue="90">The maximum number of sequences to use.</param>
		<param name="random_seed" shortName="rs" defaultValue="3976763">The random seed.</param>
		<param name="align_method" shortName="am" defaultValue="muscle">The alignment method: clustalw, muscle, kalign, t_coffee, or amap.</param>
		<param name="tcoffee_min_score" shortName="tms" defaultValue="3">Minimum support value for columns.</param>
		
		<param name="fubar_sequence_limit" shortName="fsl" defaultValue="90">The maximum number of sequences to use in FUBAR.</param>
		<param name="omegamap_sequence_limit" shortName="osl" defaultValue="90">The maximum number of sequences to use in OmegaMap.</param>
		<param name="codeml_sequence_limit" shortName="csl" defaultValue="30">The maximum number of sequences to use in codeML.</param>
		<param name="fubar_runs" shortName="fr" defaultValue="1">The number of FUBAR runs.</param>
		<param name="omegamap_runs" shortName="or" defaultValue="1">The number of OmegaMap runs.</param>
		<param name="codeml_runs" shortName="cr" defaultValue="1">The number of codeML runs.</param>
		
		<param name="mrbayes_generations" shortName="mbg" defaultValue="1000000"></param>
		<param name="mrbayes_burnin" shortName="mbb" defaultValue="2500"></param>
		<param name="mrbayes_model" shortName="mbm" defaultValue="6"></param>
		<param name="mrbayes_rates" shortName="mbr" defaultValue="invgamma"></param>
		<param name="codeml_models" shortName="cmm" defaultValue="1 2 7 8"></param>

		<flag name="omegamap_recomb" shortName="ore">Runs OmegaMap only if recombination is detected in the master file.</flag>
		<param name="omegamap_iterations" shortName="oi" defaultValue="2500">Number of OmegaMap iterations.</param>

		<flag name="skip_pull_docker_images" shortName="sdi">Use this flag to skip the pull-docker-images task.</flag>
		<param name="version_utilities" shortName="vu" defaultValue="0.9.0" global="true">Version of the pegi3s/utilities to use.</param>
		<param name="version_tcoffee" shortName="vt" defaultValue="12.00.7" global="true">Version of the pegi3s/tcoffee to use.</param>
		<param name="version_alter" shortName="va" defaultValue="1.3.4" global="true">Version of the pegi3s/alter to use.</param>
		<param name="version_seqkit" shortName="vs" defaultValue="0.12.0" global="true">Version of the pegi3s/seqkit to use.</param>
		<param name="version_mrbayes" shortName="vm" defaultValue="3.2.6" global="true">Version of the pegi3s/mrbayes to use.</param>
		<param name="version_phipack" shortName="vp" defaultValue="latest" global="true">Version of the pegi3s/phipack to use.</param>
		<param name="version_omegamap" shortName="vo" defaultValue="latest" global="true">Version of the pegi3s/omegamap to use.</param>
		<param name="version_hyphy" shortName="vh" defaultValue="2.3.14" global="true">Version of the pegi3s/hyphy to use.</param>
		<param name="version_paml" shortName="vpa" defaultValue="4.9" global="true">Version of the pegi3s/paml to use.</param>
	</params>

	<tasks>
		<task id="pull-docker-images" params="skip_pull_docker_images" if="[ -v ${skip_pull_docker_images} ]">
			docker pull pegi3s/utilities:${version_utilities}
			docker pull pegi3s/tcoffee:${version_tcoffee}
			docker pull pegi3s/alter:${version_alter}
			docker pull pegi3s/seqkit:${version_seqkit}
			docker pull pegi3s/mrbayes:${version_mrbayes}
			docker pull pegi3s/phipack:${version_phipack}
			docker pull pegi3s/omegamap:${version_omegamap}
			docker pull pegi3s/hyphy:${version_hyphy}
			docker pull pegi3s/paml:${version_paml}
		</task>

		<task id="initialization" after="pull-docker-images">
			rm -rf ${working_dir}/input/*

			mkdir -p ${working_dir}/input/1_original ${working_dir}/input/2_modified ${working_dir}/input/3_renamed_headers ${working_dir}/input/4_subsets ${working_dir}/input/5_translated ${working_dir}/input/6_aligned ${working_dir}/input/7_backtranslated ${working_dir}/input/8_master_alignment ${working_dir}/input/9_master_alignment_renamed

			mkdir -p ${working_dir}/input/2_modified_excluded/1_ambiguous_positions ${working_dir}/input/2_modified_excluded/2_min_sequences

			mkdir -p ${working_dir}/input/10_gapped_alignment/1_alignment ${working_dir}/input/10_gapped_alignment/2_gapped_alignment ${working_dir}/input/10_gapped_alignment/3_dna_filtered_fasta

			cp ${input_dir}/* ${working_dir}/input/1_original
			cp ${input_dir}/* ${working_dir}/input/2_modified

			mkdir -p ${working_dir}/pss_subsets ${working_dir}/run_lists ${working_dir}/results/tabulated
		</task>

		<task id="prepare-input-files" after="initialization">
			docker run --rm -v ${host_working_dir}/:/data pegi3s/utilities:${version_utilities} bash -c "batch_fasta_remove_stop_codons /data/input/2_modified/*"
			docker run --rm -v ${host_working_dir}/:/data pegi3s/utilities:${version_utilities} bash -c "batch_fasta_remove_line_breaks /data/input/2_modified/*"
		</task>

		<foreach id="check-input-files" after="prepare-input-files" of="command" in="ls ${working_dir}/input/2_modified/*" as="file">
			FILENAME=$(basename -- "${file}")

			docker run --rm -v ${host_working_dir}/:/data pegi3s/utilities:${version_utilities} check_multiple_3 /data/input/2_modified/$FILENAME
			if [ ! $? -eq 0 ]; then
				echo "Error: $FILENAME contains non-multiple of 3 sequences, which are not allowed. Fix this issue and resume the pipeline execution."
				exit 1
			fi

			${scripts_dir}/check_ambiguous_positions.sh $file
			if [ ! $? -eq 0 ]; then
				echo "Warning: $FILENAME contains ambiguous nucleotide positions. Sequences are removed from this file before running the analysis."
				mv $file ${working_dir}/input/2_modified_excluded/1_ambiguous_positions/$FILENAME
				${scripts_dir}/remove_sequences_with_ambiguous_positions.sh ${working_dir}/input/2_modified_excluded/1_ambiguous_positions/$FILENAME $file
			fi

			# Ignore FASTA files with less than 4 sequences
			COUNT_SEQS=$(grep '>' $file | wc -l);
			if [ $COUNT_SEQS -lt 4 ]; then
				mv $file ${working_dir}/input/2_modified_excluded/2_min_sequences/$FILENAME
			fi

			exit 0
		</foreach>

		<foreach id="rename-headers" after="check-input-files" of="command" in="ls ${working_dir}/input/2_modified/*" as="file">
			FILENAME=$(basename -- "${file}")
			
			${scripts_dir}/replace_and_save_headers.sh $file ${working_dir}/input/3_renamed_headers
		</foreach>

		<foreach id="create-subset" after="*rename-headers" of="command" in="ls ${working_dir}/input/2_modified/*" as="file" params="sequence_limit random_seed">
			FILENAME=$(basename -- "${file}")

			${scripts_dir}/create_subset.sh ${FILENAME}.renamed ${working_dir}/input/3_renamed_headers ${working_dir}/input/4_subsets ${sequence_limit} 1 ${random_seed}
			mv ${working_dir}/input/4_subsets/${FILENAME}.renamed.1 ${working_dir}/input/4_subsets/${FILENAME}
		</foreach>

		<foreach id="translate-dna-to-protein" after="*create-subset" of="command" in="ls ${working_dir}/input/2_modified/*" as="file">
			FILENAME=$(basename -- "${file}")

			docker run --rm -v ${host_working_dir}/:/data pegi3s/tcoffee:${version_tcoffee} t_coffee -other_pg seq_reformat -in /data/input/4_subsets/${FILENAME} -action +translate -output fasta_seq > ${working_dir}/input/5_translated/$FILENAME
		</foreach>

		<foreach id="align-protein-sequences" after="*translate-dna-to-protein" of="command" in="ls ${working_dir}/input/2_modified/*" as="file" params="align_method">
			FILENAME=$(basename -- "${file}")

			lowercase_align_method=$(echo ${align_method} | tr "[:upper:]" "[:lower:]")

			case ${lowercase_align_method} in
				"clustalw" )
					lowercase_align_method=clustalw_msa ;;
				"muscle" )
					lowercase_align_method=muscle_msa ;;
				"kalign" )
					lowercase_align_method=kalign_msa ;;
				"t_coffee" )
					lowercase_align_method=t_coffee_msa ;;
				"amap" )
					lowercase_align_method=amap_msa ;;
				* )
					echo "Unknown alignment program ${lowercase_align_method}."
					exit 1
					;;
			esac

			docker run --rm -v ${host_working_dir}:/data pegi3s/tcoffee:${version_tcoffee} t_coffee /data/input/5_translated/${FILENAME} -method=${lowercase_align_method} -output=aln,fasta_aln,html,score_ascii -run_name /data/input/6_aligned/${FILENAME}
		</foreach>

		<foreach id="back-translation" after="*align-protein-sequences" of="command" in="ls ${working_dir}/input/2_modified/*" as="file">
			FILENAME=$(basename -- "${file}")
			FILENAME_WITHOUT_EXT="${FILENAME%.*}"

			docker run --rm -v ${host_working_dir}:/data pegi3s/tcoffee:${version_tcoffee} t_coffee -other_pg seq_reformat -in /data/input/4_subsets/${FILENAME} -in2 /data/input/6_aligned/${FILENAME_WITHOUT_EXT}.aln -action +thread_dna_on_prot_aln -output clustalw > ${working_dir}/input/7_backtranslated/${FILENAME_WITHOUT_EXT}.backtranslated.aln
		</foreach>
		
		<foreach id="clustal-to-fasta" after="*back-translation" of="command" in="ls ${working_dir}/input/2_modified/*" as="file">
			FILENAME=$(basename -- "${file}")
			FILENAME_WITHOUT_EXT="${FILENAME%.*}"

			docker run --rm -v ${host_working_dir}:/data pegi3s/alter:${version_alter} -i /data/input/7_backtranslated/${FILENAME_WITHOUT_EXT}.backtranslated.aln -o /data/input/8_master_alignment/${FILENAME} -ia -of FASTA -oo Linux -op GENERAL

			docker run --rm -v ${host_working_dir}/:/data pegi3s/utilities:${version_utilities} fasta_remove_line_breaks /data/input/8_master_alignment/${FILENAME}
		</foreach>
		
		<foreach id="rename-headers-back" after="*clustal-to-fasta" of="command" in="ls ${working_dir}/input/2_modified/*" as="file">
			FILENAME=$(basename -- "${file}")

			${scripts_dir}/put_headers_back.sh ${working_dir}/input/8_master_alignment/${FILENAME} ${working_dir}/input/3_renamed_headers/${FILENAME}.headers_map ${working_dir}/input/9_master_alignment_renamed/${FILENAME}
		</foreach>
		
		<foreach id="phipack-master-alignment" after="*clustal-to-fasta" of="command" in="ls ${working_dir}/input/2_modified/*" as="file">
			FILENAME=$(basename -- "${file}")
			FILENAME_WITHOUT_EXT="${FILENAME%.*}"

			rm -rf ${working_dir}/input/results/master_alignment/phipack/${FILENAME}
			mkdir -p ${working_dir}/input/results/master_alignment/phipack/${FILENAME}

			docker run --rm -v ${host_working_dir}/:/data pegi3s/phipack:${version_phipack} bash -c "Phi -f /data/input/8_master_alignment/${FILENAME} -p 1000 -w 80 -o > /data/input/results/master_alignment/phipack/${FILENAME}/phipack.log"

			if [ $? -eq 0 ]; then
				${scripts_dir}/phipack_check_evidence.sh ${working_dir}/input/results/master_alignment/phipack/${FILENAME} phipack.log
			fi
		</foreach>
		
		<foreach id="check-master-alignment-recombination" after="*phipack-master-alignment,*create-pss-subsets" of="command" in="ls ${working_dir}/input/2_modified/*" as="file" params="omegamap_recomb">
			FILENAME=$(basename -- "${file}")
			
			if [ ! -z ${omegamap_recomb} ]; then
				if [ -f ${working_dir}/input/results/master_alignment/phipack/${FILENAME}/phipack.log.summary ]; then
					count=$(cat ${working_dir}/input/results/master_alignment/phipack/${FILENAME}/phipack.log.summary | grep "^No evidence" | wc -l)
					if [ $count -eq 1 ]; then
						rm -rf ${working_dir}/pss_subsets/${FILENAME}/original_alignment/omegamap/fasta
					fi
				fi
			fi

			if [ -d ${working_dir}/pss_subsets/${FILENAME}/original_alignment/omegamap/fasta ]; then
				mkdir -p ${working_dir}/pss_subsets/${FILENAME}/run_lists

				rm -f ${working_dir}/pss_subsets/${FILENAME}/run_lists/omegamap
				touch ${working_dir}/pss_subsets/${FILENAME}/run_lists/omegamap

				for SUBSET in $(ls ${working_dir}/pss_subsets/${FILENAME}/original_alignment/omegamap/fasta); do
					echo "${working_dir}/pss_subsets/${FILENAME}/original_alignment/omegamap,$SUBSET" >> ${working_dir}/pss_subsets/${FILENAME}/run_lists/omegamap
				done 
			fi
		</foreach>
		
		<foreach id="rename-headers-pss-subsets" after="*check-master-alignment-recombination" of="command" in="ls ${working_dir}/input/2_modified/*" as="file">
			FILENAME=$(basename -- "${file}")
			
			for METHOD in fubar codeml; do
				if [ -d ${working_dir}/pss_subsets/${FILENAME}/original_alignment/${METHOD}/fasta ]; then
					rm -rf ${working_dir}/pss_subsets/${FILENAME}/original_alignment/${METHOD}/fasta_renamed
					mkdir -p ${working_dir}/pss_subsets/${FILENAME}/original_alignment/${METHOD}/fasta_renamed
					
					for SUBSET in $(ls ${working_dir}/pss_subsets/${FILENAME}/original_alignment/${METHOD}/fasta); do
						${scripts_dir}/put_headers_back.sh ${working_dir}/pss_subsets/${FILENAME}/original_alignment/${METHOD}/fasta/${SUBSET} ${working_dir}/input/3_renamed_headers/${FILENAME}.headers_map ${working_dir}/pss_subsets/${FILENAME}/original_alignment/${METHOD}/fasta_renamed/${SUBSET}
					done 
				fi			
			done
		</foreach>

		<task id="gather-omegamap-run-lists" after="check-master-alignment-recombination">
			rm -f ${working_dir}/run_lists/omegamap
			cat ${working_dir}/pss_subsets/*/run_lists/omegamap > ${working_dir}/run_lists/omegamap
		</task>

		<foreach id="run-omegamap" after="gather-omegamap-run-lists" of="command" in="cat ${working_dir}/run_lists/omegamap" as="line" params="omegamap_iterations">
			FILE_PATH=$(echo $line | cut -d',' -f1)
			FILENAME=$(echo $line | cut -d',' -f2)
			REPLACEMENT=$(echo "${working_dir}" | sed -e 's#\/#\\\/#g')
			FILE_PATH_DOCKER=$(echo $FILE_PATH | sed -e "s#${REPLACEMENT}\/##g")

			rm -rf ${FILE_PATH}/results/${FILENAME}
			mkdir -p ${FILE_PATH}/results/${FILENAME}

			docker run --rm -v ${host_working_dir}/:/data pegi3s/omegamap:${version_omegamap} analyze /data/${FILE_PATH_DOCKER}/fasta/${FILENAME} /data/${FILE_PATH_DOCKER}/results/${FILENAME} ${omegamap_iterations}
			
			${scripts_dir}/omegamap_process_results.sh ${FILE_PATH}/results/${FILENAME} ${FILENAME}
		</foreach>

		<foreach id="create-pss-subsets" after="*clustal-to-fasta" of="command" in="ls ${working_dir}/input/2_modified/*" as="file" params="omegamap_sequence_limit fubar_sequence_limit codeml_sequence_limit omegamap_runs fubar_runs codeml_runs random_seed">
			FILENAME=$(basename -- "${file}")

			rm -rf ${working_dir}/pss_subsets/${FILENAME}
			mkdir -p ${working_dir}/pss_subsets/${FILENAME}/original_alignment/fubar/fasta
			
			${scripts_dir}/create_subset.sh ${FILENAME} ${working_dir}/input/8_master_alignment ${working_dir}/pss_subsets/${FILENAME}/original_alignment/fubar/fasta ${fubar_sequence_limit} ${fubar_runs} ${random_seed}

			mkdir -p ${working_dir}/pss_subsets/${FILENAME}/original_alignment/omegamap/fasta
			
			${scripts_dir}/create_subset.sh ${FILENAME} ${working_dir}/input/8_master_alignment ${working_dir}/pss_subsets/${FILENAME}/original_alignment/omegamap/fasta ${omegamap_sequence_limit} ${omegamap_runs} ${random_seed}

			mkdir -p ${working_dir}/pss_subsets/${FILENAME}/original_alignment/codeml/fasta
			
			${scripts_dir}/create_subset.sh ${FILENAME} ${working_dir}/input/8_master_alignment ${working_dir}/pss_subsets/${FILENAME}/original_alignment/codeml/fasta ${codeml_sequence_limit} ${codeml_runs} ${random_seed}
		</foreach>

		<foreach id="mrbayes-filter-alignment" after="*align-protein-sequences" of="command" in="ls ${working_dir}/input/2_modified/*" as="file" params="tcoffee_min_score">
			FILENAME=$(basename -- "${file}")
			FILENAME_WITHOUT_EXT="${FILENAME%.*}"
			FILENAME_WITHOUT_ALL_EXT=$(echo ${FILENAME} | cut -d'.' -f1)

			cp ${working_dir}/input/6_aligned/${FILENAME_WITHOUT_EXT}.aln ${working_dir}/input/10_gapped_alignment/1_alignment/${FILENAME_WITHOUT_EXT}.aln

			docker run --rm -v ${host_working_dir}:/data pegi3s/tcoffee:${version_tcoffee} t_coffee -infile /data/input/10_gapped_alignment/1_alignment/${FILENAME_WITHOUT_EXT}.aln -evaluate -output tcs_column_filter${tcoffee_min_score} -run_name /data/input/10_gapped_alignment/2_gapped_alignment/${FILENAME_WITHOUT_EXT}

			mv ${working_dir}/input/10_gapped_alignment/2_gapped_alignment/${FILENAME_WITHOUT_ALL_EXT}.tcs_column_filter${tcoffee_min_score} ${working_dir}/input/10_gapped_alignment/2_gapped_alignment/${FILENAME_WITHOUT_EXT}.aln
		</foreach>

		<foreach id="mrbayes-reconstruct-dna-files" after="*mrbayes-filter-alignment" of="command" in="ls ${working_dir}/input/2_modified/*" as="file">
			FILENAME=$(basename -- "${file}")
			FILENAME_WITHOUT_EXT="${FILENAME%.*}"

			rm -f ${working_dir}/10_gapped_alignment/3_dna_filtered_fasta/${FILENAME_WITHOUT_EXT}.fasta

			export VERSION_ALTER=${version_alter}
			export VERSION_SEQKIT=${version_seqkit}
			export VERSION_PEGI3S_UTILITIES=${version_utilities}

			${scripts_dir}/create_mrbayes_gapped_dna_alignment.sh ${working_dir}/input/6_aligned/${FILENAME_WITHOUT_EXT}.aln  ${working_dir}/input/10_gapped_alignment/2_gapped_alignment/${FILENAME_WITHOUT_EXT}.aln ${working_dir}/input/4_subsets/${FILENAME} ${working_dir}/input/10_gapped_alignment/3_dna_filtered_fasta/${FILENAME_WITHOUT_EXT}.fasta
		</foreach>

		<foreach id="mrbayes-create-pss-subsets" after="*create-pss-subsets,*mrbayes-reconstruct-dna-files" of="command" in="ls ${working_dir}/input/2_modified/*" as="file">
			FILENAME=$(basename -- "${file}")
			FILENAME_WITHOUT_EXT="${FILENAME%.*}"

			mkdir -p ${working_dir}/pss_subsets/${FILENAME}/run_lists

			rm -rf ${working_dir}/pss_subsets/${FILENAME}/gapped_alignment
			
			rm -f ${working_dir}/pss_subsets/${FILENAME}/run_lists/mrbayes
			touch ${working_dir}/pss_subsets/${FILENAME}/run_lists/mrbayes
			
			for METHOD in fubar codeml; do
				mkdir -p ${working_dir}/pss_subsets/${FILENAME}/gapped_alignment/${METHOD}/fasta

				for SUBSET in $(ls ${working_dir}/pss_subsets/${FILENAME}/original_alignment/${METHOD}/fasta); do
					cat ${working_dir}/pss_subsets/${FILENAME}/original_alignment/${METHOD}/fasta/${SUBSET}| grep '>' | sed -e 's/>//g' > ${working_dir}/pss_subsets/${FILENAME}/gapped_alignment/${METHOD}/fasta/ids_${SUBSET}
					
					docker run --rm -v ${host_working_dir}/:/data pegi3s/seqkit:${version_seqkit} grep -f /data/pss_subsets/${FILENAME}/gapped_alignment/${METHOD}/fasta/ids_${SUBSET} /data/input/10_gapped_alignment/3_dna_filtered_fasta/${FILENAME_WITHOUT_EXT}.fasta -o /data/pss_subsets/${FILENAME}/gapped_alignment/${METHOD}/fasta/${SUBSET}
					
					rm ${working_dir}/pss_subsets/${FILENAME}/gapped_alignment/${METHOD}/fasta/ids_*
					
					echo "${working_dir}/pss_subsets/${FILENAME}/gapped_alignment/${METHOD},$SUBSET" >> ${working_dir}/pss_subsets/${FILENAME}/run_lists/mrbayes
				done 
			done
		</foreach>

		<task id="gather-mrbayes-run-lists" after="mrbayes-create-pss-subsets">
			rm -f ${working_dir}/run_lists/mrbayes
			cat ${working_dir}/pss_subsets/*/run_lists/mrbayes > ${working_dir}/run_lists/mrbayes
		</task>

		<foreach id="prepare-mrbayes-files" after="gather-mrbayes-run-lists" of="command" in="cat ${working_dir}/run_lists/mrbayes" as="line" params="mrbayes_generations mrbayes_burnin mrbayes_model mrbayes_rates">
			FILE_PATH=$(echo $line | cut -d',' -f1)
			FILENAME=$(echo $line | cut -d',' -f2)
			REPLACEMENT=$(echo "${working_dir}" | sed -e 's#\/#\\\/#g')
			FILE_PATH_DOCKER=$(echo $FILE_PATH | sed -e "s#${REPLACEMENT}##g")

			rm -rf ${FILE_PATH}/mrbayes/${FILENAME}
			mkdir -p ${FILE_PATH}/mrbayes/${FILENAME}

			docker run --rm -v ${host_working_dir}/:/data pegi3s/alter:${version_alter} -i /data/${FILE_PATH_DOCKER}/fasta/${FILENAME} -o /data/${FILE_PATH_DOCKER}/mrbayes/${FILENAME}/${FILENAME}.nex -ia -of NEXUS -oo Linux -op MrBayes
			
			${scripts_dir}/mrbayes_append_nexus_file.sh ${FILE_PATH}/mrbayes/${FILENAME}/${FILENAME}.nex ${mrbayes_generations} ${mrbayes_burnin} ${mrbayes_model} ${mrbayes_rates}
		</foreach>
		
		<foreach id="run-mrbayes" after="*prepare-mrbayes-files" of="command" in="cat ${working_dir}/run_lists/mrbayes" as="line">
			FILE_PATH=$(echo $line | cut -d',' -f1)
			FILENAME=$(echo $line | cut -d',' -f2)
			REPLACEMENT=$(echo "${working_dir}" | sed -e 's#\/#\\\/#g')
			FILE_PATH_DOCKER=$(echo $FILE_PATH | sed -e "s#${REPLACEMENT}##g")

			mv ${FILE_PATH}/mrbayes/${FILENAME}/${FILENAME}.nex ${FILE_PATH}/mrbayes/${FILENAME}/mrbayes_input.nex

			docker run --rm -v ${host_working_dir}/${FILE_PATH_DOCKER}/mrbayes/${FILENAME}/:/data pegi3s/mrbayes:${version_mrbayes} mb /data/mrbayes_input.nex

			if [ ! -f "${FILE_PATH}/mrbayes/${FILENAME}/mrbayes_input.nex.con.tre" ]; then
				echo "Error in run-mrbayes: mrbayes_input.nex.con.tre was not created."
				exit 1
			else
				${scripts_dir}/mrbayes_get_tree.sh mrbayes_input.nex.con.tre ${FILE_PATH}/mrbayes/${FILENAME}
			fi
		</foreach>

		<foreach id="create-fubar-codeml-run-lists" after="run-mrbayes" of="command" in="ls ${working_dir}/input/2_modified/*" as="file">
			FILENAME=$(basename -- "${file}")

			mkdir -p ${working_dir}/pss_subsets/${FILENAME}/run_lists

			for METHOD in fubar codeml; do
				rm -f ${working_dir}/pss_subsets/${FILENAME}/run_lists/${METHOD}
				touch ${working_dir}/pss_subsets/${FILENAME}/run_lists/${METHOD}

				for SUBSET in $(ls ${working_dir}/pss_subsets/${FILENAME}/original_alignment/${METHOD}/fasta); do
					echo "${working_dir}/pss_subsets/${FILENAME}/original_alignment/${METHOD},$SUBSET" >> ${working_dir}/pss_subsets/${FILENAME}/run_lists/${METHOD}
				done
			done
		</foreach>
		
		<task id="gather-fubar-codeml-run-lists" after="create-fubar-codeml-run-lists">
			rm -f ${working_dir}/run_lists/fubar
			cat ${working_dir}/pss_subsets/*/run_lists/fubar > ${working_dir}/run_lists/fubar

			rm -f ${working_dir}/run_lists/codeml
			cat ${working_dir}/pss_subsets/*/run_lists/codeml > ${working_dir}/run_lists/codeml
		</task>

		<foreach id="run-fubar" after="gather-fubar-codeml-run-lists" of="command" in="cat ${working_dir}/run_lists/fubar" as="line">
			FILE_PATH=$(echo $line | cut -d',' -f1)
			FILENAME=$(echo $line | cut -d',' -f2)
			REPLACEMENT=$(echo "${working_dir}" | sed -e 's#\/#\\\/#g')
			FILE_PATH_DOCKER=$(echo $FILE_PATH | sed -e "s#${REPLACEMENT}##g")
			
			rm -rf ${FILE_PATH}/results/${FILENAME}
			mkdir -p ${FILE_PATH}/results/${FILENAME}
			
			MR_BAYES_PATH=$(echo ${FILE_PATH} | sed 's/original_alignment/gapped_alignment/g')
			
			${scripts_dir}/fubar_prepare_input.sh ${FILENAME} ${FILE_PATH}/fasta ${MR_BAYES_PATH}/mrbayes/${FILENAME}/mrbayes_tree_without_branch_lengths.tre ${FILE_PATH}/results/${FILENAME}

			${scripts_dir}/fubar_create_hyphy_setttings_file.sh ${FILE_PATH}/results/${FILENAME}/HYPHY_settings "/data/${FILE_PATH_DOCKER}/results/${FILENAME}/${FILENAME}.fna"

			docker run --rm -v ${host_working_dir}/:/data pegi3s/hyphy:${version_hyphy} bash -c "cd /data/${FILE_PATH_DOCKER}/results/${FILENAME}/; cat HYPHY_settings | HYPHYMP > ${FILENAME}.results"

			${scripts_dir}/fubar_process_results.sh ${FILE_PATH}/results/${FILENAME}/${FILENAME}.results
		</foreach>

		<foreach id="check-codeml-limit" after="gather-fubar-codeml-run-lists" of="command" in="cat ${working_dir}/run_lists/codeml" as="line">
			FILE_PATH=$(echo $line | cut -d',' -f1)
			FILENAME=$(echo $line | cut -d',' -f2)
			REPLACEMENT=$(echo "${working_dir}" | sed -e 's#\/#\\\/#g')
			FILE_PATH_DOCKER=$(echo $FILE_PATH | sed -e "s#${REPLACEMENT}##g")
            
            mkdir -p ${FILE_PATH}/fasta_checked
            rm -f ${FILE_PATH}/fasta_checked/${FILENAME}
            ${scripts_dir}/codeml_check_limit.sh ${FILENAME} ${FILE_PATH}/fasta ${FILE_PATH}/fasta_checked/${FILENAME}
		</foreach>

		<foreach id="run-codeml" after="*check-codeml-limit" of="command" in="cat ${working_dir}/run_lists/codeml" as="line" params="codeml_models">
			FILE_PATH=$(echo $line | cut -d',' -f1)
			FILENAME=$(echo $line | cut -d',' -f2)
			REPLACEMENT=$(echo "${working_dir}" | sed -e 's#\/#\\\/#g')
			FILE_PATH_DOCKER=$(echo $FILE_PATH | sed -e "s#${REPLACEMENT}##g")

			MR_BAYES_PATH_DOCKER=$(echo ${FILE_PATH_DOCKER} | sed 's/original_alignment/gapped_alignment/g')
			
			rm -rf ${FILE_PATH}/results/${FILENAME}
			mkdir -p ${FILE_PATH}/results/${FILENAME}

			${scripts_dir}/codeml_prepare_ctl_file.sh ${FILE_PATH}/results/${FILENAME}/codeml.ctl "${codeml_models}" "/data/fasta_checked/${FILENAME}" "/tree/mrbayes/${FILENAME}/mrbayes_tree_without_branch_lengths.tre" "codeml.out"

			# Mount shorter file paths to avoid codeML failing due to long file paths
			docker run --rm -v ${host_working_dir}/${FILE_PATH_DOCKER}/:/data -v ${host_working_dir}/${MR_BAYES_PATH_DOCKER}:/tree -w /data/results/${FILENAME} pegi3s/paml:${version_paml} codeml.ctl

			mv ${FILE_PATH}/results/${FILENAME}/codeml.out ${FILE_PATH}/results/${FILENAME}/${FILENAME}.codeml.out

			${scripts_dir}/codeml_process_results.sh ${FILE_PATH}/fasta_checked/${FILENAME} ${FILE_PATH}/results/${FILENAME}/${FILENAME}.codeml.out ${FILE_PATH}/results/${FILENAME}/${FILENAME}.results_PSS.list
		</foreach>

		<task id="gather-phipack-run-lists" after="gather-fubar-codeml-run-lists,gather-omegamap-run-lists">
			cat ${working_dir}/run_lists/codeml ${working_dir}/run_lists/omegamap ${working_dir}/run_lists/fubar > ${working_dir}/run_lists/phipack
		</task>
		
		<foreach id="run-phipack" after="gather-phipack-run-lists" of="command" in="cat ${working_dir}/run_lists/phipack" as="line">
			FILE_PATH=$(echo $line | cut -d',' -f1)
			FILENAME=$(echo $line | cut -d',' -f2)
			REPLACEMENT=$(echo "${working_dir}" | sed -e 's#\/#\\\/#g')
			FILE_PATH_DOCKER=$(echo $FILE_PATH | sed -e "s#${REPLACEMENT}##g")

			rm -rf ${FILE_PATH}/phipack/${FILENAME}
			mkdir -p ${FILE_PATH}/phipack/${FILENAME}

			docker run --rm -v ${host_working_dir}/:/data pegi3s/phipack:${version_phipack} bash -c "Phi -f /data/${FILE_PATH_DOCKER}/fasta/${FILENAME} -p 1000 -w 80 -o > /data/${FILE_PATH_DOCKER}/phipack/${FILENAME}/phipack.log"

			if [ $? -eq 0 ]; then
				${scripts_dir}/phipack_check_evidence.sh ${FILE_PATH}/phipack/${FILENAME} phipack.log
			fi
		</foreach>
        
		<foreach id="tabulate-results" after="run-omegamap, run-codeml, run-fubar" of="command" in="ls ${working_dir}/input/2_modified/*" as="file">
			FILENAME=$(basename -- "${file}")

			rm -f ${working_dir}/results/tabulated/${FILENAME}

			${scripts_dir}/tabulate_results.sh ${working_dir}/pss_subsets ${FILENAME} ${working_dir}/results/tabulated/${FILENAME}

			export VERSION_ALTER=${version_alter}
			export VERSION_PEGI3S_UTILITIES=${version_utilities}
			${scripts_dir}/results_get_gaps_and_support_values.sh ${FILENAME} ${working_dir} ${host_working_dir}
		</foreach>
	</tasks>

	<metadata>
		<task-description id="pull-docker-images">Pulls the necessary Docker images from the pegi3s/dockerfiles project.</task-description>
		<task-description id="initialization">Initialices the working directory.</task-description>
		<task-description id="prepare-input-files">Removes stop codons and line breaks from all input files.</task-description>
		<task-description id="gather-omegamap-run-lists">Joins all omegaMap run lists into a single run list.</task-description>
		<task-description id="gather-mrbayes-run-lists">Joins all Mr. Bayes run lists into a single run list.</task-description>
		<task-description id="gather-fubar-codeml-run-lists">Joins all FUBAR and codeML run lists into a single run list.</task-description>
		<task-description id="gather-phipack-run-lists">Joins all phipack run lists into a single run list.</task-description>
		<task-description id="check-input-files">Verifies if any of the input files contains ambiguous nucleotide positions or non-multiple of 3 sequences. If so, the pipeline execution is stopped and the problematic files must be manually fixed before continuing.</task-description>
		<task-description id="rename-headers">Renames the sequence headers to be C1, C2, ..., Cn in each FASTA file.</task-description>
		<task-description id="create-subset">Extracts a random subset of sequences according to the sequence limit specified to create the master set of sequences.</task-description>
		<task-description id="translate-dna-to-protein">Translates each master set of sequences from DNA to protein.</task-description>
		<task-description id="align-protein-sequences">Aligns the translated master sets of sequences.</task-description>
		<task-description id="back-translation">Translates each aligned master set of sequences from protein to DNA. These are called master DNA alignments.</task-description>
		<task-description id="clustal-to-fasta">Converts the master DNA alignments to FASTA format.</task-description>
		<task-description id="rename-headers-back">Puts the original sequence headers in the master DNA aligned FASTA files.</task-description>
		<task-description id="phipack-master-alignment">Runs phipack on each master DNA alignment.</task-description>
		<task-description id="check-master-alignment-recombination">If the omegaMap recombination flag is present, checks the phipack results for each master DNA alignment in order to decide if omegaMap must be executed.</task-description>
		<task-description id="rename-headers-pss-subsets">Puts the original sequence headers in the PSS subset files.</task-description>
		<task-description id="run-omegamap">Runs omegaMap for each one of the PSS subsets.</task-description>
		<task-description id="create-pss-subsets">Creates the PSS subsets for CodeML, omegaMap, and FUBAR, according to the number of sequences and replicas specified for each method.</task-description>
		<task-description id="mrbayes-filter-alignment">Filters the master protein alignment to remove low confidence positions, according to the value specified.</task-description>
		<task-description id="mrbayes-reconstruct-dna-files">Converts the filtered protein alignments to DNA.</task-description>
		<task-description id="mrbayes-create-pss-subsets">Creates the same subsets used by CodeML, omegaMap, and FUBAR using the filtered DNA files. These are the files used by MrBayes to produce a Bayesian phylogenetic tree that is used by FUBAR and CodeML.</task-description>
		<task-description id="prepare-mrbayes-files">Creates the MrBayes input files.</task-description>
		<task-description id="run-mrbayes">Runs FUBAR for each one of the PSS subsets.</task-description>
		<task-description id="create-fubar-codeml-run-lists">Creates the FUBAR and codeML run lists.</task-description>
		<task-description id="run-fubar">Runs FUBAR for each one of the PSS subsets.</task-description>
		<task-description id="check-codeml-limit">Checks the codeML limits.</task-description>
		<task-description id="run-codeml">Runs codeML for each one of the PSS subsets.</task-description>
		<task-description id="run-phipack">Runs phipack for each one of the PSS subsets.</task-description>
		<task-description id="tabulate-results">Gathers the results of all PSS methods for each input FASTA file into a tabular format.</task-description>
	</metadata>
</pipeline>