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annot.nf
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annot.nf
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#!/usr/bin/env nextflow
VERSION = "1.0.2"
/*
Author: Sascha Steinbiss <[email protected]>
Copyright (c) 2014-2016 Genome Research Ltd
Permission to use, copy, modify, and distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.
THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/
genome_file = file(params.inseq)
ref_annot = file(params.ref_dir + "/" + params.ref_species + "/annotation.gff3")
ref_seq = file(params.ref_dir + "/" + params.ref_species + "/genome.fasta")
ref_dir = file(params.ref_dir)
go_obo = file(params.GO_OBO)
ncrna_models = file(params.NCRNA_MODELS)
extrinsic_cfg = file(params.AUGUSTUS_EXTRINSIC_CFG)
omcl_gfffile = file(params.ref_dir + "/" + params.ref_species + "/annotation.gff3")
omcl_gaffile = file(params.ref_dir + "/" + params.ref_species + "/go.gaf")
omcl_pepfile = file(params.ref_dir + "/" + params.ref_species + "/proteins.fasta")
augustus_modeldir = file(params.ref_dir + "/" + params.ref_species)
log.info ""
log.info "C O M P A N I O N ~ version " + VERSION
log.info "query : ${params.inseq}"
log.info "reference : ${params.ref_species}"
log.info "reference directory : ${params.ref_dir}"
if (params.dist_dir) {
distDir = new File(params.dist_dir)
if(distDir.exists() && distDir.isFile()) {
exit 1, "cannot create output path: ${params.dist_dir} -- already exists as file"
}
if(!distDir.exists() && !distDir.mkdirs()) {
exit 1, "cannot create output path: ${params.dist_dir} -- check file system permissions"
}
if(!distDir.isDirectory()) {
exit 1, "cannot prepare output path: ${params.dist_dir} -- aborting"
}
log.info "output directory : ${params.dist_dir}"
}
log.info ""
// INPUT SANITIZATION
// ==================
if (params.truncate_input_headers) {
process truncate_input_headers {
input:
file genome_file
output:
file 'truncated.fasta' into truncated_genome_file
"""
truncate_header.lua < ${genome_file} > truncated.fasta
"""
}
} else {
genome_file.into { truncated_genome_file }
}
process sanitize_input {
input:
file 'truncated.fasta' from truncated_genome_file
output:
file 'sanitized.fasta' into sanitized_genome_file
"""
sed 's/['\\''+&= ]/_/g' truncated.fasta | trim_wildcards.lua > sanitized.fasta
"""
}
// PSEUDOCHROMOSOME CONTIGUATION
// =============================
if (params.do_contiguation) {
ref_chr = file(params.ref_dir + "/" + params.ref_species + "/chromosomes.fasta")
process contiguate_pseudochromosomes {
afterScript 'rm -rf Ref.* Res.*'
input:
file sanitized_genome_file
file ref_chr
file ref_dir
output:
file 'pseudo.pseudochr.fasta' into pseudochr_seq
file 'pseudo.pseudochr.agp' into pseudochr_agp
file 'pseudo.scafs.fasta' into scaffolds_seq
file 'pseudo.scafs.agp' into scaffolds_agp
file 'pseudo.contigs.fasta' into contigs_seq
file 'ref_target_mapping.txt' into ref_target_mapping
"""
abacas2.nonparallel.sh \
"${ref_chr}" "${sanitized_genome_file}" "${params.ABACAS_MATCH_SIZE}" \
"${params.ABACAS_MATCH_SIM}" 0 3000
abacas_combine.lua . pseudo "${ref_dir}" "${params.ref_species}" \
"${params.GENOME_PREFIX}" "${params.ABACAS_BIN_CHR}" \
"${params.GENOME_PREFIX}"
"""
}
} else {
process prepare_noncontiguated_input {
input:
file sanitized_genome_file
output:
file 'pseudo.pseudochr.fasta' into pseudochr_seq
file 'pseudo.pseudochr.agp' into pseudochr_agp
file 'pseudo.scafs.fasta' into scaffolds_seq
file 'pseudo.scafs.agp' into scaffolds_agp
file 'pseudo.contigs.fasta' into contigs_seq
"""
no_abacas_prepare.lua ${sanitized_genome_file} pseudo
"""
}
}
// fork important output streams
pseudochr_seq.into{ pseudochr_seq_tRNA
pseudochr_seq_ncRNA
pseudochr_seq_ratt
pseudochr_seq_augustus
pseudochr_seq_augustus_ctg
pseudochr_seq_snap
pseudochr_seq_make_gaps
pseudochr_seq_make_dist_1
pseudochr_seq_make_dist_2
pseudochr_seq_splitsplice
pseudochr_seq_pseudogene
pseudochr_seq_integrate
pseudochr_seq_tmhmm
pseudochr_seq_orthomcl
pseudochr_seq_exonerate }
scaffolds_seq.into{ scaffolds_seq_augustus
scaffolds_seq_make_gaps
scaffolds_seq_make_dist_1
scaffolds_seq_make_dist_2 }
scaffolds_agp.into{ scaffolds_agp_augustus
scaffolds_agp_rnaseq
scaffolds_agp_make_gaps
scaffolds_agp_make_dist }
pseudochr_agp.into{ pseudochr_agp_augustus
pseudochr_agp_rnaseq
pseudochr_agp_make_gaps
pseudochr_agp_make_dist }
// TRNA PREDICTION
// ===============
process predict_tRNA {
input:
file 'pseudo.pseudochr.fasta' from pseudochr_seq_tRNA
output:
file 'aragorn.gff3' into trnas
"""
aragorn -t pseudo.pseudochr.fasta > out
grep -E -C2 '(nucleotides|Sequence)' out > 1
aragorn_to_gff3.lua < 1 > 2
gt gff3 -sort -tidy -retainids 2 > aragorn.gff3
"""
}
// NCRNA PREDICTION
// ================
process press_ncRNA_cms {
input:
val ncrna_models
output:
file 'models.cm*' into ncrna_cmindex
"""
cp ${ncrna_models} ./models.cm
cmpress -F models.cm
"""
}
pseudochr_seq_ncRNA.splitFasta( by: 5, file: true).set { ncrna_genome_chunk }
process predict_ncRNA {
input:
file 'chunk' from ncrna_genome_chunk
file ncrna_models from ncrna_cmindex.first()
output:
file 'cm_out' into cmtblouts
"""
cmsearch --cpu 1 --tblout cm_out --cut_ga models.cm chunk
"""
}
process merge_ncrnas {
cache 'deep'
input:
file 'cmtblout' from cmtblouts.collectFile()
output:
file 'ncrna.gff3' into ncrnafile
"""
infernal_to_gff3.lua < ${cmtblout} > 1
gt gff3 -sort -tidy -retainids 1 > ncrna.gff3
"""
}
// PROTEIN-DNA ALIGNMENT
// =====================
if (params.run_exonerate) {
process make_exonerate_index {
input:
file 'genome.fasta' from pseudochr_seq_exonerate.first()
output:
file 'index.esi' into exn_index_esi
file 'index.esd' into exn_index_esd
file 'genome.fasta' into exn_index_fasta
"""
fasta2esd --softmask no genome.fasta index.esd
esd2esi index.esd index.esi --translate yes
"""
}
process make_ref_peps {
cache 'deep'
input:
file ref_annot
file ref_seq
output:
file 'ref.pep' into ref_pep
"""
gt gff3 -sort -tidy -retainids ${ref_annot} > 1
gt extractfeat -matchdescstart -seqfile ${ref_seq} \
-join -type CDS -translate -retainids 1 > ref.pep
"""
}
exn_prot_chunk = ref_pep.splitFasta( by: 200, file: true)
process run_exonerate {
cache 'deep'
// this process can fail for rogue exonerate processes
errorStrategy 'ignore'
time '3h'
input:
file 'index.esi' from exn_index_esi.first()
file 'index.esd' from exn_index_esd.first()
file 'genome.fasta' from exn_index_fasta.first()
file 'prot.fasta' from exn_prot_chunk
output:
file 'exn_out' into exn_results
"""
get_unused_port.sh > port
reaper.sh exonerate-server --port `cat port` --input index.esi &
sleep 10
exonerate -E false --model p2g --showvulgar no --showalignment no \
--showquerygff no --showtargetgff yes --percent 80 --geneseed 250 \
--ryo \"AveragePercentIdentity: %pi\n\" prot.fasta \
localhost:`cat port` > exn_out
kill `cat exonerate-server.pid`
rm -f exonerate-server.pid
"""
}
process exonerate_make_hints {
cache 'deep'
input:
file 'exnout' from exn_results.collectFile()
output:
file 'augustus.hints' into exn_hints
script:
"""
exonerate2hints.pl \
--source=P --maxintronlen=${params.AUGUSTUS_HINTS_MAXINTRONLEN} \
--in=${exnout} \
--out=augustus.hints
"""
}
} else {
process exonerate_empty_hints {
output:
file 'augustus.hints' into exn_hints
"""
touch augustus.hints
"""
}
}
// RATT
// ====
if (params.run_ratt) {
process ratt_make_ref_embl {
input:
file ref_annot
file ref_seq
val go_obo
output:
file '*.embl' into ref_embl
"""
gff3_to_embl.lua -o ${ref_annot} ${go_obo} Foo ${ref_seq}
"""
}
process run_ratt {
afterScript 'rm -rf Reference* Sequences Query query.*'
input:
file 'in*.embl' from ref_embl
file 'pseudo.pseudochr.fasta' from pseudochr_seq_ratt
output:
file 'Out*.final.embl' into ratt_result
file 'Out*.Report.txt' into ratt_reports
"""
touch Out.0.Report.txt
start.ratt.sh . pseudo.pseudochr.fasta Out ${params.RATT_TRANSFER_TYPE}
"""
}
process ratt_to_gff3 {
input:
file 'in*.embl' from ratt_result
file 'in*.report' from ratt_reports
output:
file 'ratt.gff3' into ratt_gff3
"""
echo '##gff-version 3' > ratt.gff3
ratt_embl_to_gff3.lua in*.embl | \
gt gff3 -sort -retainids -tidy > \
ratt.tmp.gff3
if [ -s ratt.tmp.gff3 ]; then
ratt_remove_problematic.lua ratt.tmp.gff3 in*report | \
gt gff3 -sort -retainids -tidy > ratt.gff3;
fi
"""
}
} else {
process ratt_empty_models {
output:
file 'result.gff3' into ratt_gff3
"""
echo '##gff-version 3' > result.gff3
"""
}
}
// TRANSCRIPT EVIDENCE PREPARATION
// ===============================
if (params.TRANSCRIPT_FILE) {
transcript_evidence = file(params.TRANSCRIPT_FILE)
process transform_input_gtf {
input:
file 'transcripts.gtf' from transcript_evidence
file 'pseudochr.agp' from pseudochr_agp_rnaseq
output:
file 'transcripts_transformed.gtf' into transcript_evidence_transformed
"""
LC_ALL='C' sort -k 1,1 -k 4,4n transcripts.gtf | uniq > 1
transform_gtf_with_agp.lua 1 pseudochr.agp > transcripts_transformed.gtf
"""
}
process prepare_transcript_hints {
input:
file 'transcripts.gtf' from transcript_evidence_transformed
output:
file 'transcripts.hints' into trans_hints
"""
LC_ALL='C' sort -k 1,1 -k 4,4n transcripts.gtf | uniq | \
cufflinks_to_hints.lua > transcripts.hints
"""
}
} else {
process transcript_empty_hints {
output:
file 'transcripts.hints' into trans_hints
"""
touch transcripts.hints
"""
}
}
// HINTS PREPARATION
// =================
process merge_hints {
cache 'deep'
input:
file 'hints.exon.txt' from exn_hints
file 'hints.trans.txt' from trans_hints
output:
set stdout, file('hints.txt') into all_hints
"""
touch hints.txt
cat hints.exon.txt hints.trans.txt > hints.concatenated.txt
if [ -s hints.concatenated.txt ] ; then
mv hints.concatenated.txt hints.txt;
echo -n '--alternatives-from-evidence=false --hintsfile=augustus.hints';
fi
"""
}
// AUGUSTUS
// ========
process run_augustus_pseudo {
cache 'deep'
input:
set val(hintsline), file('augustus.hints') from all_hints
file 'pseudo.pseudochr.fasta' from pseudochr_seq_augustus
val extrinsic_cfg
file augustus_modeldir
output:
file 'augustus.gff3' into augustus_pseudo_gff3
"""
echo "##gff-version 3\n" > augustus.full.tmp.2;
AUGUSTUS_CONFIG_PATH=${augustus_modeldir} \
augustus \
--species=augustus_species \
--stopCodonExcludedFromCDS=false \
--protein=off --codingseq=off --strand=both \
--genemodel=${params.AUGUSTUS_GENEMODEL} --gff3=on \
${hintsline} \
--noInFrameStop=true \
--extrinsicCfgFile=${extrinsic_cfg} \
pseudo.pseudochr.fasta > augustus.full.tmp
augustus_to_gff3.lua < augustus.full.tmp \
| gt gff3 -sort -tidy -retainids > 1
if [ -s 1 ]; then
gt select -mingenescore ${params.AUGUSTUS_SCORE_THRESHOLD} 1 \
> augustus.full.tmp.2;
fi
augustus_mark_partial.lua augustus.full.tmp.2 > augustus.gff3
"""
}
process run_augustus_contigs {
input:
file 'pseudo.contigs.fasta' from contigs_seq
file 'pseudo.scaffolds.agp' from scaffolds_agp_augustus
file 'pseudo.scaffolds.fasta' from scaffolds_seq_augustus
file 'pseudo.pseudochr.agp' from pseudochr_agp_augustus
file 'pseudo.pseudochr.fasta' from pseudochr_seq_augustus_ctg
file augustus_modeldir
output:
file 'augustus.scaf.pseudo.mapped.gff3' into augustus_ctg_gff3
"""
echo "##gff-version 3\n" > augustus.ctg.tmp.2;
AUGUSTUS_CONFIG_PATH=${augustus_modeldir} \
augustus --species=augustus_species \
--stopCodonExcludedFromCDS=false \
--protein=off --codingseq=off --strand=both --genemodel=partial \
--gff3=on \
--noInFrameStop=true \
pseudo.contigs.fasta > augustus.ctg.tmp
augustus_to_gff3.lua < augustus.ctg.tmp \
| gt gff3 -sort -tidy -retainids > 1
if [ -s 1 ]; then
gt select -mingenescore ${params.AUGUSTUS_SCORE_THRESHOLD} 1 \
> augustus.ctg.tmp.2;
fi
augustus_mark_partial.lua augustus.ctg.tmp.2 > augustus.ctg.gff3
transform_gff_with_agp.lua \
augustus.ctg.gff3 \
pseudo.scaffolds.agp \
pseudo.contigs.fasta \
pseudo.scaffolds.fasta | \
gt gff3 -sort -tidy -retainids > \
augustus.ctg.scaf.mapped.gff3
transform_gff_with_agp.lua \
augustus.ctg.scaf.mapped.gff3 \
pseudo.pseudochr.agp \
pseudo.scaffolds.fasta \
pseudo.pseudochr.fasta | \
gt gff3 -sort -tidy -retainids > \
augustus.scaf.pseudo.mapped.gff3
if [ ! -s augustus.scaf.pseudo.mapped.gff3 ]; then
echo '##gff-version 3' > augustus.scaf.pseudo.mapped.gff3
fi
"""
}
if (params.run_snap) {
snap_model = file(params.ref_dir + "/" + params.ref_species + "/snap.hmm")
process run_snap {
input:
file 'pseudo.pseudochr.fasta' from pseudochr_seq_snap
file 'snap.hmm' from snap_model
output:
file 'snap.gff3' into snap_gff3
"""
echo '##gff-version 3' > snap.gff3
snap -gff -quiet snap.hmm pseudo.pseudochr.fasta > snap.tmp
snap_gff_to_gff3.lua snap.tmp > snap.tmp.2
if [ -s 1 ]; then
gt gff3 -sort -tidy -retainids snap.tmp.2 > snap.gff3;
fi
"""
}
} else {
process make_empty_snap {
output:
file 'snap.gff3' into snap_gff3
"""
echo '##gff-version 3' > snap.gff3
"""
}
}
process merge_genemodels {
cache 'deep'
input:
file 'augustus.full.gff3' from augustus_pseudo_gff3
file 'augustus.ctg.gff3' from augustus_ctg_gff3
file 'snap.full.gff3' from snap_gff3
file 'ratt.full.gff3' from ratt_gff3
output:
file 'merged.gff3' into merged_gff3
"""
unset GT_RETAINIDS && \
gt gff3 -fixregionboundaries -retainids no -sort -tidy \
augustus.full.gff3 augustus.ctg.gff3 snap.full.gff3 ratt.full.gff3 \
> merged.pre.gff3 && \
export GT_RETAINIDS=yes
if [ ! -s merged.pre.gff3 ]; then
echo '##gff-version 3' > merged.pre.gff3
fi
# avoid huge gene clusters
gt select -maxgenelength ${params.MAX_GENE_LENGTH} merged.pre.gff3 > merged.gff3
"""
}
process integrate_genemodels {
cache 'deep'
afterScript 'rm -rf sequence.fasta.*'
input:
file 'merged.gff3' from merged_gff3
file 'sequence.fasta' from pseudochr_seq_integrate
output:
file 'integrated.gff3' into integrated_gff3
script:
if (params.WEIGHT_FILE.length() > 0)
"""
integrate_gene_calls.lua -w ${params.WEIGHT_FILE} -s sequence.fasta < merged.gff3 | \
gt gff3 -sort -tidy -retainids > integrated.gff3
"""
else
"""
integrate_gene_calls.lua -s sequence.fasta < merged.gff3 | \
gt gff3 -sort -tidy -retainids > integrated.gff3
"""
}
if (params.fix_polycistrons) {
process fix_polycistrons {
input:
file 'integrated.gff3' from integrated_gff3
output:
file 'integrated.fixed.sorted.gff3' into integrated_gff3_processed
"""
if [ ! -s integrated.gff3 ]; then
echo '##gff-version 3' > integrated.gff3
fi
fix_polycistrons.lua integrated.gff3 > integrated.fixed.gff3
# make sure final output is sorted
gt gff3 -sort -tidy -retainids \
integrated.fixed.gff3 > integrated.fixed.sorted.gff3
"""
}
} else {
integrated_gff3.into { integrated_gff3_processed }
}
process remove_exons {
input:
file 'integrated.gff3' from integrated_gff3_processed
output:
file 'integrated_clean.gff3' into integrated_gff3_clean
"""
if [ ! -s integrated.gff3 ]; then
echo '##gff-version 3' > integrated.gff3
fi
remove_exons.lua integrated.gff3 > integrated_clean.gff3
"""
}
if (params.do_pseudo) {
process pseudogene_indexing {
input:
file 'ref.peps.fasta' from omcl_pepfile
output:
file 'prot_index*' into pseudochr_last_index
"""
tantan -p -r0.02 ref.peps.fasta | lastdb -p -c prot_index
"""
}
pseudochr_seq_pseudogene.into{ pseudochr_seq_pseudogene_align; pseudochr_seq_pseudogene_calling }
pseudochr_seq_pseudogene_align.splitFasta( by: 3, file: true).set { pseudogene_align_chunk }
process pseudogene_last {
input:
file 'chunk.fasta' from pseudogene_align_chunk
file prot_index from pseudochr_last_index.first()
output:
file 'last.out' into pseudochr_last_out
"""
lastal -R01 -pBL80 -F15 -e400 -m10 -f0 prot_index chunk.fasta > last.out
"""
}
process pseudogene_calling {
cache 'deep'
input:
file 'pseudochr.fasta' from pseudochr_seq_pseudogene_calling
file 'genes.gff3' from integrated_gff3_clean
file 'last.out' from pseudochr_last_out.collectFile()
output:
file 'genes_and_pseudo.gff3' into gff3_with_pseudogenes
"""
# reconstruct frameshifted candidates from output
pseudo_merge_last.lua last.out pseudochr.fasta > last_gff.gff3
# merge with gene models
gt gff3 -sort -tidy -retainids last_gff.gff3 genes.gff3 > last_and_genes.gff3
if [ ! -s last_and_genes.gff3 ]; then
echo '##gff-version 3' > last_and_genes.gff3
fi
pseudo_merge_with_genes.lua last_and_genes.gff3 pseudochr.fasta > out_tmp.gff3
gt gff3 -sort -retainids -tidy out_tmp.gff3 > genes_and_pseudo.gff3
"""
}
} else {
gff3_with_pseudogenes = integrated_gff3_clean
}
// MERGE ALL GENES TO FINAL SET AND CLEANUP
// ========================================
process merge_structural {
cache 'deep'
input:
file 'ncrna.gff3' from ncrnafile
file 'trna.gff3' from trnas
file 'integrated.gff3' from gff3_with_pseudogenes
output:
file 'structural.full.gff3' into genemodels_gff3
"""
gt gff3 -sort -tidy ncrna.gff3 integrated.gff3 trna.gff3 \
> structural.full.gff3
"""
}
// ADD GAPS AND ADJUST GENES NOT TO SPAN GAPS
// ==========================================
process add_gap_features {
input:
file 'merged_in.gff3' from genemodels_gff3
file 'pseudo.scaffolds.agp' from scaffolds_agp_make_gaps
file 'pseudo.scaffolds.fasta' from scaffolds_seq_make_gaps
file 'pseudo.pseudochr.agp' from pseudochr_agp_make_gaps
file 'pseudo.pseudochr.fasta' from pseudochr_seq_make_gaps
output:
file 'merged_out.gff3' into genemodels_with_gaps_gff3
"""
set -ev
make_contig_features_from_agp.lua pseudo.scaffolds.agp "within scaffold" | \
gt gff3 -fixregionboundaries -sort -tidy -retainids > contigs.gff3
transform_gff_with_agp.lua contigs.gff3 \
pseudo.pseudochr.agp pseudo.scaffolds.fasta \
pseudo.pseudochr.fasta "between scaffolds" | \
gt gff3 -fixregionboundaries -sort -tidy -retainids > contigs2.gff3
if [ ! -s merged_in.gff3 ]; then
echo '##gff-version 3' > merged_in.gff3
fi
gt merge -force -o merged_out.gff3 \
merged_in.gff3 contigs2.gff3
"""
}
process split_splice_models_at_gaps {
input:
file 'input.gff3' from genemodels_with_gaps_gff3
file 'pseudo.pseudochr.fasta' from pseudochr_seq_splitsplice
output:
file 'merged_out.gff3' into genemodels_with_gaps_split_gff3
"""
# sort
gt gff3 -sort -retainids -tidy < input.gff3 > tmp2
# split genes at inter-scaffold gaps
split_genes_at_gaps.lua tmp2 | \
gt gff3 -sort -retainids -tidy > tmp3
# splice genes at inter-contig gaps, get rid of short partials
splice_genes_at_gaps_new.lua tmp3 | \
gt gff3 -sort -retainids -tidy | \
gt select -rule_files ${FILTER_SHORT_PARTIALS_RULE} > tmp4
# get rid of genes still having stop codons
filter_genes_with_stop_codons.lua \
tmp4 pseudo.pseudochr.fasta | \
gt gff3 -sort -retainids -tidy > merged_out.gff3
"""
}
process add_polypeptides {
input:
file 'input.gff3' from genemodels_with_gaps_split_gff3
output:
file 'output.gff3' into genemodels_with_polypeptides_gff3
script:
if (params.alphanumeric_ids)
"""
create_polypeptides.lua -r input.gff3 ${params.GENOME_PREFIX} \
"${params.CHR_PATTERN}" | gt gff3 -sort -retainids -tidy > output.gff3
"""
else
"""
create_polypeptides.lua input.gff3 ${params.GENOME_PREFIX} \
"${params.CHR_PATTERN}" | gt gff3 -sort -retainids -tidy > output.gff3
"""
}
// TMHMM
// =====
// disabled for now for license reasons
/* process run_tmhmm {
input:
file 'input.gff3' from genemodels_with_polypeptides_gff3
file 'pseudo.pseudochr.fasta' from pseudochr_seq_tmhmm
output:
file 'output.gff3' into genemodels_with_tmhmm_gff3
"""
gt extractfeat -type CDS -join -translate \
-seqfile pseudo.pseudochr.fasta -matchdescstart \
input.gff3 > proteins.fas
tmhmm --noplot < proteins.fas > tmhmm.out
tmhmm_to_gff3.lua tmhmm.out input.gff3 | \
gt gff3 -sort -retainids -tidy > output.gff3
"""
} */
// ORTHOMCL AND FUNCTIONAL TRANSFER
// ================================
genemodels_with_polypeptides_gff3.into{ genemodels_for_omcl_proteins; genemodels_for_omcl_annot }
process get_proteins_for_orthomcl {
input:
file 'input.gff3' from genemodels_for_omcl_proteins
file 'pseudo.pseudochr.fasta' from pseudochr_seq_orthomcl
output:
file 'input.gff3' into genemodels_orthomcl_gff3
file 'proteins.fas' into proteins_target
"""
gt extractfeat -type CDS -translate -join -retainids \
-seqfile pseudo.pseudochr.fasta -matchdescstart < input.gff3 \
| truncate_header.lua > proteins.fas
gt extractfeat -type pseudogenic_exon -translate \
-join -retainids \
-seqfile pseudo.pseudochr.fasta -matchdescstart < input.gff3 \
| truncate_header.lua >> proteins.fas
"""
}
proteins_target.into{ proteins_orthomcl
proteins_pfam
refcomp_protein_in
proteins_output }
process make_ref_input_for_orthomcl {
input:
file omcl_pepfile
output:
file 'out.gg' into gg_file
file 'shortname' into shortname
file 'mapped.fasta' into mapped_fasta
script:
"""
truncate_header.lua < ${omcl_pepfile} > pepfile.trunc
ln -s pepfile.trunc mapped.fasta
make_gg_line.lua ${params.ref_species} mapped.fasta > out.gg
echo "${params.ref_species}" > shortname
"""
}
process make_target_input_for_orthomcl {
input:
file 'pepfile.fas' from proteins_orthomcl
output:
file 'out.gg' into gg_file_ref
file 'shortname' into shortname_ref
file 'mapped.fasta' into mapped_fasta_ref
"""
truncate_header.lua < pepfile.fas > pepfile.trunc
ln -s pepfile.trunc mapped.fasta
make_gg_line.lua ${params.GENOME_PREFIX} mapped.fasta > out.gg
echo "${params.GENOME_PREFIX}" > shortname
"""
}
gg_file.mix(gg_file_ref).collectFile().set { full_gg }
shortname.mix(shortname_ref).collectFile().set { full_shortnames }
mapped_fasta.mix(mapped_fasta_ref).collectFile().set { full_mapped_fasta }
full_mapped_fasta.into{ full_mapped_fasta_for_index; full_mapped_fasta_for_query }
process blast_for_orthomcl_formatdb {
cache 'deep'
input:
file 'mapped.fasta' from full_mapped_fasta_for_index
output:
file 'mapped.fasta' into full_mapped_fasta_indexed
file 'mapped.fasta.phr' into full_mapped_fasta_indexed_phr
file 'mapped.fasta.psq' into full_mapped_fasta_indexed_psq
file 'mapped.fasta.pin' into full_mapped_fasta_indexed_pin
"""
makeblastdb -dbtype prot -in mapped.fasta
"""
}
proteins_orthomcl_blast_chunk = full_mapped_fasta_for_query.splitFasta( by: 50, file: true)
process blast_for_orthomcl {
cache 'deep'
input:
file 'mapped_chunk.fasta' from proteins_orthomcl_blast_chunk
file 'mapped.fasta' from full_mapped_fasta_indexed.first()
file 'mapped.fasta.phr' from full_mapped_fasta_indexed_phr.first()
file 'mapped.fasta.psq' from full_mapped_fasta_indexed_psq.first()
file 'mapped.fasta.pin' from full_mapped_fasta_indexed_pin.first()
output:
file 'blastout' into orthomcl_blastout
"""
blastall -p blastp -W 4 -F 'm S' -v 100000 -b 100000 -d mapped.fasta -m 8 \
-i mapped_chunk.fasta > blastout
"""
}
process run_orthomcl {
cache 'deep'
input:
file 'blastout' from orthomcl_blastout.collectFile()
file 'ggfile' from full_gg
output:
file 'orthomcl_out' into orthomcl_cluster_out
"""
orthomcl.pl --inflation 1.5 --mode 3 \
--blast_file blastout \
--gg_file ggfile
cp `find . -mindepth 1 -name all_orthomcl.out` orthomcl_out
"""
}
orthomcl_cluster_out.into{ orthomcl_cluster_out_annot; result_ortho }
process annotate_orthologs {
cache 'deep'
input:
file 'orthomcl_out' from orthomcl_cluster_out_annot
file 'input.gff3' from genemodels_for_omcl_annot
file 'gff_ref.gff3' from omcl_gfffile
file 'gaf_ref.gaf' from omcl_gaffile
output:
file 'with_func.gff3' into gff3_with_ortho_transferred
file 'orthomcl.gaf' into gaf_with_ortho_transferred
"""
# ensure sorting of input file
gt gff3 -sort -retainids -tidy input.gff3 > input.gff3.sorted
# annotate GFF with ortholog clusters and members
map_clusters_gff.lua input.gff3.sorted orthomcl_out > with_clusters.gff3
# transfer functional annotation from orthologs
transfer_annotations_from_gff.lua with_clusters.gff3 \
gff_ref.gff3 > with_func.gff3
# transfer GOs from orthologs GAF
transfer_annotations_from_gaf.lua with_func.gff3 \
gaf_ref.gaf ${params.DB_ID} \
${params.TAXON_ID} > orthomcl.gaf