From 7e7ad652da0faac714016bea5058440dcbf48bfa Mon Sep 17 00:00:00 2001
From: Cedric Cabau <cedric.cabau@inra.fr>
Date: Fri, 23 Mar 2018 09:22:05 +0000
Subject: [PATCH] runMeta now accepts a list of assembly fasta files
---
trunk/runMeta | 208 ++++++++++++++++++++++++++++++++++++--------------
1 file changed, 150 insertions(+), 58 deletions(-)
diff --git a/trunk/runMeta b/trunk/runMeta
index 663ac5d..b59046e 100755
--- a/trunk/runMeta
+++ b/trunk/runMeta
@@ -8,6 +8,7 @@ use File::Basename;
use File::Compare;
use File::Path qw(make_path remove_tree);
use POSIX qw(strftime);
+use List::Util qw(uniq);
use lib ("$FindBin::RealBin/bin");
use AsmUtils;
use Report;
@@ -21,7 +22,10 @@ my @backup_options = @ARGV;
my @getOptions = (
['help',undef,undef,0],
['o|outdir','s',undef,1], # DIRECTORY Ouput directory
- ['drap-dirs','s{,}',undef,0], # DRAP DIRECTORIES
+ ['drap-dirs','s{,}',undef,0], # DRAP DIRECTORIES
+ ['R1','s{,}',undef,0], # FASTQ for RMBT step if drap-dirs is empty
+ ['R2','s{,}',undef,0], # FASTQ Mates for RMBT step if drap-dirs is empty
+ ['assemblies','s{,}',undef,0], # Assemblies to meta-assemble if drap-dirs is empty
['input-type','s','transcripts',0], # Primary assembly target type [transcripts]
['input-cov','i',undef,0], # Primary assembly target coverage [lowest coverage value]
['s|strand','s',undef,0], # For strand specific sequencing data: FR or RF for paired reads; F or R for single
@@ -82,13 +86,26 @@ map { pod2usage("$_ is required") if ($required->{$_} && ! defined($opt->{$_}))
map { my $key = $_; s/.+\|//; s/-/_/g; $opt->{$_} = delete($opt->{$key}) } keys %$opt;
## allowing comma-separated lists of values as well as multiple occurrences of the options
-@{$opt->{drap_dirs}} = @ARGV unless (@{$opt->{drap_dirs}}); # compatibility with drap-v1.8
-@{$opt->{drap_dirs}} = split(/,/, join(',', @{$opt->{drap_dirs}}));
+if (@{$opt->{assemblies}}) {
+ @{$opt->{assemblies}} = split(/,/, join(',', @{$opt->{assemblies}}));
+} else {
+ @{$opt->{drap_dirs}} = @ARGV unless ($opt->{drap_dirs}); # compatibility with drap-v1.8
+ @{$opt->{drap_dirs}} = split(/,/, join(',', @{$opt->{drap_dirs}}));
+ for(@{$opt->{drap_dirs}}){ s|/$|| };
+}
+if (@{$opt->{R1}}) {
+ @{$opt->{R1}} = uniq(split(/,/, join(',', @{$opt->{R1}})));
+}
+if (@{$opt->{R2}}) {
+ @{$opt->{R2}} = uniq(split(/,/, join(',', @{$opt->{R2}})));
+ printOutMessage("NUMBER of UNIQ R1 and R2 FASTQ FILES DIFFERS") unless (scalar(@{$opt->{R1}}) == scalar(@{$opt->{R2}}));
+}
# initialize drap path
-$opt->{binpath} = "$FindBin::RealBin/bin";
-$opt->{cfgpath} = "$FindBin::RealBin/cfg";
-$opt->{reportpath} = "$FindBin::RealBin/report";
+$opt->{binpath} = "$FindBin::RealBin/bin";
+$opt->{cfgpath} = "$FindBin::RealBin/cfg";
+$opt->{pluginspath} = "$FindBin::RealBin/plugins";
+$opt->{reportpath} = "$FindBin::RealBin/report";
# CFG_FILE param checking
if (defined($opt->{cfg_file})) {
@@ -98,6 +115,7 @@ if (defined($opt->{cfg_file})) {
}
# expand PATH and ENV variables
+$ENV{PATH} = join(':', glob("$opt->{pluginspath}/*")).":".$ENV{PATH};
$ENV{PATH} = $opt->{binpath}.":".$ENV{PATH};
$opt->{env}->{PATH} = $ENV{PATH};
set_extended_path( $opt->{cfg_file} );
@@ -107,11 +125,23 @@ set_env_variables( $opt->{cfg_file}, $opt );
# PARAMS CHECKINGS
#------------------
my $paired_asm;
-unless (scalar(@{$opt->{drap_dirs}}) > 1) { printOutMessage("AT LEAST TWO runDrap DIRECTORIES ARE MANDATORY\n") };
-foreach (@{$opt->{drap_dirs}}) {
- unless (-d $_){ printOutMessage("NO SUCH DRAP DIRECTORY: $_"); }
- unless (-f "$_/.drap_conf.json"){ printOutMessage("CANNOT FIND DRAP CONFIG FILE .drap_conf.json INSIDE DRAP DIRECTORY: $_"); }
- $paired_asm += get_cfg_param($_, 'paired');
+if (@{$opt->{drap_dirs}}) {
+ unless (scalar(@{$opt->{drap_dirs}}) > 1) { printOutMessage("AT LEAST TWO runDrap DIRECTORIES ARE MANDATORY\n") };
+ foreach (@{$opt->{drap_dirs}}) {
+ unless (-d $_){ printOutMessage("NO SUCH DRAP DIRECTORY: $_"); }
+ unless (-f "$_/.drap_conf.json"){ printOutMessage("CANNOT FIND DRAP CONFIG FILE .drap_conf.json INSIDE DRAP DIRECTORY: $_"); }
+ $paired_asm += get_cfg_param($_, 'paired');
+ }
+ if (@{$opt->{assemblies}}) { printOutMessage("OPTIONS drap-dirs AND assemblies ARE MUTUALLY EXCLUSIVE"); }
+ if (@{$opt->{R1}}) { printOutMessage("OPTIONS drap-dirs AND R1 ARE MUTUALLY EXCLUSIVE"); }
+} else {
+ unless (@{$opt->{assemblies}}) { printOutMessage("PLEASE GIVE runDrap DIRECTORIES OR assembly FILES TO META-ASSEMBLE"); }
+ unless (scalar(@{$opt->{assemblies}}) > 1) { printOutMessage("AT LEAST TWO assembly FILES ARE MANDATORY\n") };
+ unless (@{$opt->{R1}}) { printOutMessage("OPTION R1 IS REQUIRED WITH assemblies OPTION"); }
+ map { printOutMessage("NO SUCH FASTQ FILE: $_") unless (-f $_) } @{$opt->{R1}};
+ if (@{$opt->{R2}}) {
+ map { printOutMessage("NO SUCH FASTQ FILE: $_") unless (-f $_) } @{$opt->{R2}};
+ }
}
if (defined($opt->{ref})) {
@@ -122,11 +152,13 @@ if (defined($opt->{strand})) {
if ($opt->{strand} ne 'F' && $opt->{strand} ne 'R' && $opt->{strand} ne 'RF' && $opt->{strand} ne 'FR') {
printOutMessage("UNKNOWN STRAND-SPECIFIC library TYPE. Please choose \'R\', \'F\' for SINGLE reads, \'RF\' or \'FR\' for PAIRED reads");
}
- foreach my $drap_dir (@{$opt->{drap_dirs}}) {
- my $used_strand = get_cfg_param($drap_dir, 'strand');
- printf("Warning: --strand parameter differs from STRAND-SPECIFIC library TYPE use for assembly %s (%s)\n",
- $drap_dir, $used_strand ? "--strand $used_strand" : "no strand parameter") if ($opt->{strand} ne $used_strand
- );
+ if (@{$opt->{drap_dirs}}) {
+ foreach my $drap_dir (@{$opt->{drap_dirs}}) {
+ my $used_strand = get_cfg_param($drap_dir, 'strand');
+ printf("Warning: --strand parameter differs from STRAND-SPECIFIC library TYPE use for assembly %s (%s)\n",
+ $drap_dir, $used_strand ? "--strand $used_strand" : "no strand parameter") if ($opt->{strand} ne $used_strand
+ );
+ }
}
}
@@ -175,16 +207,21 @@ my $clean_msg;
if ($opt->{restart}) {
print "Check steps already executed:\n";
} else {
- print 'Run meta-assembly from '.scalar(@{$opt->{drap_dirs}})." primary assemblies\n";
+ printf("Run meta-assembly from %d primary assemblies\n", scalar(@{$opt->{drap_dirs}}) || scalar(@{$opt->{assemblies}}));
}
# convert path to absolute path for outdir and files outside outdir
-foreach my $key (qw(outdir ref cfg_file)) {
+foreach my $key (qw(outdir ref cfg_file drap_dirs assemblies R1 R2)) {
next unless (defined($opt->{$key}));
- $opt->{$key} = File::Spec->rel2abs($opt->{$key});
+ if (ref($opt->{$key}) eq 'ARRAY') {
+ for (@{$opt->{$key}}) { $_ = File::Spec->rel2abs($_) };
+ } else {
+ $opt->{$key} = File::Spec->rel2abs($opt->{$key});
+ }
}
# create output directory
+$opt->{outdir} =~ s|/$||;
mkdir($opt->{outdir}) or die "Can't create directory $opt->{outdir}\n" unless (-d $opt->{outdir});
# write command in log file
@@ -228,11 +265,18 @@ unless (-f "$opt->{dir_list}->[0]/.$opt->{step}.over" && step_complete($opt)) {
$opt->{restart} = 0;
$resubmit = $opt->{step};
}
- foreach my $drap_dir (@{$opt->{drap_dirs}}) {
- my $condition = basename($drap_dir);
- my $drap_lowest_fpkm = $opt->{input_cov} || shift(@{get_cfg_param($drap_dir, 'coverages')});
- die "Can't open file $drap_dir/$opt->{input_type}_fpkm_$drap_lowest_fpkm.fa\n" unless (-f "$drap_dir/$opt->{input_type}_fpkm_$drap_lowest_fpkm.fa");
- $opt->{cmd} .= qq(cat $drap_dir/$opt->{input_type}_fpkm_$drap_lowest_fpkm.fa | sed -e "s/^>/>${condition}_/" >> $opt->{dir_list}->[0]/all_conditions_contigs.fa\n);
+ if (@{$opt->{drap_dirs}}) {
+ foreach my $drap_dir (@{$opt->{drap_dirs}}) {
+ my $condition = basename($drap_dir);
+ my $drap_lowest_fpkm = $opt->{input_cov} || shift(@{get_cfg_param($drap_dir, 'coverages')});
+ die "Can't open file $drap_dir/$opt->{input_type}_fpkm_$drap_lowest_fpkm.fa\n" unless (-f "$drap_dir/$opt->{input_type}_fpkm_$drap_lowest_fpkm.fa");
+ $opt->{cmd} .= qq(cat $drap_dir/$opt->{input_type}_fpkm_$drap_lowest_fpkm.fa | sed -e "s/^>/>${condition}_/" >> $opt->{dir_list}->[0]/all_conditions_contigs.fa\n);
+ }
+ } else {
+ foreach my $assembly (@{$opt->{assemblies}}) {
+ (my $condition = basename($assembly)) =~ s/\.t?fn?a(sta)?$//;
+ $opt->{cmd} .= qq(cat $assembly | sed -e "s/^>/>${condition}_/" >> $opt->{dir_list}->[0]/all_conditions_contigs.fa\n);
+ }
}
$opt->{cmd} .= "touch $opt->{dir_list}->[0]/.$opt->{step}.over\n";
my $merge_metrics_file = $report_db_folder."/".$merge_analysis->get_or_create_step('Rename and merge')->get_or_create_metrics_filename('fastaAssembly');
@@ -363,8 +407,8 @@ unless (-f "$opt->{dir_list}->[2]/.$opt->{step}.over" && step_complete($opt)) {
$resubmit = $opt->{step};
}
$opt->{cmd} .= sprintf ("%s/runSamse.sh -r %s/meta_contigs.fa -f %s -o %s -m %s -t %d --index --sync%s\n",
- $opt->{binpath}, $opt->{dir_list}->[1], get_cfg_param($opt->{drap_dirs}->[0], 'alignR1')->[0], $opt->{dir_list}->[2],
- $opt->{mapper}, $opt->{env}->{n_cpu}, $opt->{local} ? ' --local' : ''
+ $opt->{binpath}, $opt->{dir_list}->[1], @{$opt->{drap_dirs}} ? get_cfg_param($opt->{drap_dirs}->[0], 'alignR1')->[0] : $opt->{R1}->[0],
+ $opt->{dir_list}->[2], $opt->{mapper}, $opt->{env}->{n_cpu}, $opt->{local} ? ' --local' : ''
);
$opt->{cmd} .= "touch $opt->{dir_list}->[2]/.$opt->{step}.over\n";
$rmbt_analysis->get_or_create_step( 'Reference indexation', 'Index the reference contig set using bwa or STAR.' );
@@ -379,7 +423,7 @@ $previous_step = $opt->{steps}->[$nstep];
$opt->{step} = $opt->{steps}->[++$nstep];
$opt->{complete} = 1;
$opt->{rmbt_ref}->{meta_rmbt} = $opt->{mapper} eq 'star' ? "$opt->{dir_list}->[2]/STAR_meta_contigs.fa" : "$opt->{dir_list}->[1]/meta_contigs.fa";
-unless (step_complete($opt) && exists($opt->{alignR1_list}) && scalar(@{[glob("$opt->{dir_list}->[2]/*.bam")]}) == scalar(@{$opt->{alignR1_list}})) {
+unless (step_complete($opt) && exists($opt->{alignR1}) && scalar(@{[glob("$opt->{dir_list}->[2]/*.bam")]}) == scalar(@{$opt->{alignR1}})) {
$opt->{complete} = 0;
if ($opt->{restart}) {
$clean_msg .= clean_rmbt_directory($opt, $opt->{dir_list}->[2]);
@@ -388,34 +432,63 @@ unless (step_complete($opt) && exists($opt->{alignR1_list}) && scalar(@{[glob("$
$resubmit = $opt->{step};
}
$opt->{cmd} .= sprintf("set reference = %s\n", $opt->{mapper} eq 'star' ? "`find $opt->{dir_list}->[2] -name STAR_meta_contigs.fa_\\*`" : "$opt->{dir_list}->[1]/meta_contigs.fa");
- foreach my $drap_dir (@{$opt->{drap_dirs}}) {
- my $paired = get_cfg_param($drap_dir, 'paired');
- my $alignR1 = get_cfg_param($drap_dir, 'alignR1');
- my $alignR2 = get_cfg_param($drap_dir, 'alignR2') if ($paired);
- for (my $i = 0 ; $i < scalar(@$alignR1) ; $i++) {
- next if (exists $opt->{rmbt_status}->{$opt->{rmbt_ref}->{meta_rmbt}}->{$alignR1->[$i]} && $opt->{rmbt_status}->{$opt->{rmbt_ref}->{meta_rmbt}}->{$alignR1->[$i]}->{status} == 1);
- next if (exists($opt->{alignR1_list}) && find_in($alignR1->[$i], $opt->{alignR1_list}));
- my $fastq = $paired ? basename($alignR1->[$i]).'/'.basename($alignR2->[$i]) : basename($alignR1->[$i]);
- $opt->{cmd} .= sprintf ("set bam = `%s/%s -r \$reference%s %s -o %s -m %s -t %d --sort_by_name --flagstat --bam%s%s`\n",
- $opt->{binpath}, $paired ? 'runSampe.sh' : 'runSamse.sh', $opt->{mapper} eq 'star' ? ' -g' : '',
- $paired ? "-1 $alignR1->[$i] -2 $alignR2->[$i]" : "-f $alignR1->[$i]",
- $opt->{dir_list}->[2], $opt->{mapper}, $opt->{env}->{n_cpu}, $opt->{filter} ? ' -y' : '', $opt->{local} ? ' --local' : ''
- );
- my $flagstat_metrics_file = $report_db_folder."/".$rmbt_analysis->get_or_create_step($opt->{mapper}, "Align reads using $opt->{mapper}.")->get_or_create_metrics_filename('flagstatLog', $fastq);
- my $flagstat_metrics_basename = basename($flagstat_metrics_file, '.json');
- if ($opt->{local}) {
- $opt->{cmd} .= "$opt->{binpath}/alignmentMetrics2json.pl \$bam.flagstat > $flagstat_metrics_file\n" ;
- } else {
- $opt->{cmd} .= "set bam_jid = `echo \$bam | sed -e 's/.*\\.\\([0-9]*\\)\\.bam/\\1/'`\n"
- ."set hold_jid = `cat $opt->{dir_list}->[2]/err_log_\$bam_jid/runSam?e.\$bam_jid.jid | tr '\\n' ,`\n"
- ."set metric = \"$opt->{binpath}/submitJob --name meta_$flagstat_metrics_basename --stdout $opt->{outdir}/err_log --stderr $opt->{outdir}/err_log --options -hold_jid \$hold_jid --binary -- '$opt->{binpath}/alignmentMetrics2json.pl \$bam.flagstat > $flagstat_metrics_file'\"\n"
- ."echo \$metric\nset metric_out = `eval \$metric`\necho \$metric_out\n"
+ if (@{$opt->{drap_dirs}}) {
+ # Allowing to perform meta from meta
+ foreach my $dir (@{$opt->{drap_dirs}}) {
+ if (get_cfg_param($dir, 'meta') == 1) {
+ if (ref(get_cfg_param($dir, 'ext_drap_dirs')) eq 'ARRAY') {
+ push(@{$opt->{ext_drap_dirs}}, @{get_cfg_param($dir, 'ext_drap_dirs')});
+ } else {
+ push(@{$opt->{ext_drap_dirs}}, @{get_cfg_param($dir, 'drap_dirs')});
+ }
+ }
+ else {
+ push(@{$opt->{ext_drap_dirs}}, $dir);
}
- if ($paired) {
- push(@{$opt->{alignR1_list}}, $alignR1->[$i]) unless (find_in($alignR1->[$i], $opt->{alignR1_list}));
- push(@{$opt->{alignR2_list}}, $alignR2->[$i]) unless (find_in($alignR2->[$i], $opt->{alignR2_list}));
+ }
+ foreach my $drap_dir (@{$opt->{ext_drap_dirs}}) {
+ my $paired = get_cfg_param($drap_dir, 'paired');
+ my $alignR1 = get_cfg_param($drap_dir, 'alignR1');
+ my $alignR2 = get_cfg_param($drap_dir, 'alignR2') if ($paired);
+ for (my $i = 0 ; $i < scalar(@$alignR1) ; $i++) {
+ next if (exists($opt->{alignR1}) && find_in($alignR1->[$i], $opt->{alignR1}));
+ push(@{$opt->{alignR1}}, $alignR1->[$i]);
+ if ($paired) {
+ push(@{$opt->{alignR2}}, $alignR2->[$i]);
+ push(@{$opt->{transrateAlignR1}}, $alignR1->[$i]) unless (find_in($alignR1->[$i], $opt->{transrateAlignR1}));
+ push(@{$opt->{transrateAlignR2}}, $alignR2->[$i]) unless (find_in($alignR2->[$i], $opt->{transrateAlignR2}));
+ } else {
+ push(@{$opt->{alignR2}}, '');
+ }
}
}
+ } else {
+ @{$opt->{alignR1}} = @{$opt->{R1}};
+ if (@{$opt->{R2}}) {
+ @{$opt->{alignR2}} = @{$opt->{R2}};
+ @{$opt->{transrateAlignR1}} = @{$opt->{R1}};
+ @{$opt->{transrateAlignR2}} = @{$opt->{R2}};
+ }
+ }
+ for (my $i = 0 ; $i < scalar(@{$opt->{alignR1}}) ; $i++) {
+ next if (exists $opt->{rmbt_status}->{$opt->{rmbt_ref}->{meta_rmbt}}->{$opt->{alignR1}->[$i]} && $opt->{rmbt_status}->{$opt->{rmbt_ref}->{meta_rmbt}}->{$opt->{alignR1}->[$i]}->{status} == 1);
+ my $paired = $opt->{alignR2}->[$i] ? 1 : 0;
+ my $fastq = $paired ? basename($opt->{alignR1}->[$i]).'/'.basename($opt->{alignR2}->[$i]) : basename($opt->{alignR1}->[$i]);
+ $opt->{cmd} .= sprintf ("set bam = `%s/%s -r \$reference%s %s -o %s -m %s -t %d --sort_by_name --flagstat --bam%s%s`\n",
+ $opt->{binpath}, $paired ? 'runSampe.sh' : 'runSamse.sh', $opt->{mapper} eq 'star' ? ' -g' : '',
+ $paired ? "-1 $opt->{alignR1}->[$i] -2 $opt->{alignR2}->[$i]" : "-f $opt->{alignR1}->[$i]",
+ $opt->{dir_list}->[2], $opt->{mapper}, $opt->{env}->{n_cpu}, $opt->{filter} ? ' -y' : '', $opt->{local} ? ' --local' : ''
+ );
+ my $flagstat_metrics_file = $report_db_folder."/".$rmbt_analysis->get_or_create_step($opt->{mapper}, "Align reads using $opt->{mapper}.")->get_or_create_metrics_filename('flagstatLog', $fastq);
+ my $flagstat_metrics_basename = basename($flagstat_metrics_file, '.json');
+ if ($opt->{local}) {
+ $opt->{cmd} .= "$opt->{binpath}/alignmentMetrics2json.pl \$bam.flagstat > $flagstat_metrics_file\n" ;
+ } else {
+ $opt->{cmd} .= "set bam_jid = `echo \$bam | sed -e 's/.*\\.\\([0-9]*\\)\\.bam/\\1/'`\n"
+ ."set hold_jid = `cat $opt->{dir_list}->[2]/err_log_\$bam_jid/runSam?e.\$bam_jid.jid | tr '\\n' ,`\n"
+ ."set metric = \"$opt->{binpath}/submitJob --name meta_$flagstat_metrics_basename --stdout $opt->{outdir}/err_log --stderr $opt->{outdir}/err_log --options -hold_jid \$hold_jid --binary -- '$opt->{binpath}/alignmentMetrics2json.pl \$bam.flagstat > $flagstat_metrics_file'\"\n"
+ ."echo \$metric\nset metric_out = `eval \$metric`\necho \$metric_out\n"
+ }
}
unless ($opt->{local} || !$opt->{cmd}) {
$opt->{cmd} .= "set all_jid = `cat $opt->{dir_list}->[2]/err_log_*/runSam?e.*.jid | tr '\\n' ,`\n"
@@ -498,7 +571,7 @@ unless ((($opt->{no_rate} && -f "$opt->{outdir}/00-META-ASSEMBLY_COMPLETE") || -
unless ($opt->{no_rate}) {
$opt->{cmd} .= "else\n" unless (-f "$opt->{outdir}/00-META-ASSEMBLY_COMPLETE");
$opt->{cmd} .= sprintf("%stransrate --assembly=%s/transcripts_fpkm_%d.fa --left=%s --right=%s --threads=%d --output=%s/transrate %s> %s/00-META-ASSEMBLY_RATING\n",
- $tab, $opt->{dir_list}->[3], $lowest_fpkm, join(',',@{$opt->{alignR1_list}}), join(',',@{$opt->{alignR2_list}}), $opt->{env}->{n_cpu},
+ $tab, $opt->{dir_list}->[3], $lowest_fpkm, join(',',@{$opt->{transrateAlignR1}}), join(',',@{$opt->{transrateAlignR2}}), $opt->{env}->{n_cpu},
$opt->{outdir}, $opt->{ref} ? "--reference=$opt->{ref} " : '', $opt->{outdir}
);
$opt->{cmd} .= "${tab}$opt->{binpath}/check_assembly.pl $opt->{outdir} $opt->{step}\n";
@@ -592,7 +665,10 @@ runMeta
runMeta \
--outdir OUTPUT_DIR \
- --drap-dirs DRAP_DIR_1,DRAP_DIR_2[,...,DRAP_DIR_n] \
+ [--drap-dirs DRAP_DIR_1,DRAP_DIR_2[,...,DRAP_DIR_n]] \
+ [--assemblies FASTA_FILE_1,FASTA_FILE_2[,...,FASTA_FILE_n]] \
+ [--R1 R1_FILE[,...,R1_FILE_n]] \
+ [--R2 R2_FILE[,...,R2_FILE_n]] \
[--strand R|F|RF|FR] \
[--ref FASTA_REF] \
[--mapper bwa|STAR] \
@@ -604,7 +680,7 @@ runMeta
=head1 DESCRIPTION
runMeta is a workflow used to merge assemblies from several samples/tissues/development stages in one assembly without redundancy.
-From two or more runDrap assemblies, it generates a meta-assembly and a report in report/DRAP_report.html.
+From two or more runDrap assemblies or input fasta files, it generates a meta-assembly and a report in report/DRAP_report.html.
=head1 OPTIONS
@@ -622,17 +698,33 @@ the previous set of options will be used to rerun the workflow.
=item B<--drap-dirs> DRAP_DIR_1,DRAP_DIR_2[,...,DRAP_DIR_n]
The paths to the runDrap output directories of assemblies to meta-assemble, comma-separated.
+Mutually exclusive with the option --assemblies.
+
+=item B<-a, --assemblies> FASTA_FILE_1,FASTA_FILE_2[,...,FASTA_FILE_n]
+
+The assembly fasta files to meta-assemble, comma-separated.
+Mutually exclusive with the option --drap-dirs.
+
+=item B<-1, --R1> R1_FILE[,...,R1_FILE_n]
+
+The R1 file(s) in FASTQ format to align at RMBT (Reads Mapped Back to Transcripts) step (gzipped or not), comma-separated.
+Mandatory with option --assemblies. Ignored with option --drap-dirs.
+
+=item B<-2, --R2> R2_FILE[,...,R2_FILE_n]
+
+The R2 file(s) in FASTQ format to align at RMBT step (gzipped or not), comma-separated.
+Ignored with option --drap-dirs.
=item B<--input-type> coding_transcripts|transcripts
runDrap assembly target type: coding_transcripts or transcripts. Associated with the input-cov parameter,
indicates from which fasta files inside each runDrap output directories runMeta will be performed.
-The default type is transcripts.
+The default type is transcripts. Ignored with option --assemblies.
=item B<--input-cov> INTEGER
runDrap assembly target coverage. By default, runMeta is performed from transcripts_fpkm_$lowest.fa files
-found inside runDrap directories with $lowest equal to the lowest fpkm value.
+found inside runDrap directories with $lowest equal to the lowest fpkm value. Ignored with option --assemblies.
=item B<-s, --strand> FR|RF|F|R
@@ -644,7 +736,7 @@ Fasta file with knowns proteins or transcripts to align with contigs using Exone
=item B<-m, --mapper> bwa|star
-Mapper to perform the RMBT step (Reads Mapped Back to Transcripts).
+Mapper to perform the RMBT step.
Available mappers are bwa and star.
The default mapper is bwa.
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