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drop trinity from de novo assembly pipeline #168

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Nov 15, 2020
Merged

drop trinity from de novo assembly pipeline #168

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3e8a2e1
drop trinity from de novo assembly pipeline
tomkinsc Nov 13, 2020
c2dfb6d
Merge branch 'master' into ct-drop-trinity
tomkinsc Nov 14, 2020
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4 changes: 1 addition & 3 deletions docs/description.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -37,8 +37,7 @@ Viral genome assembly
~~~~~~~~~~~~~~~~~~~~~

The filtered and trimmed reads are subsampled to at most 100,000 pairs.
*de novo* assemby is performed using Trinity_. SPAdes_ is also offered as
an alternative *de novo* assembler.
*de novo* assemby is performed using SPAdes_.
Reference-assisted assembly improvements follow (contig scaffolding, orienting, etc.)
with MUMMER_ and MUSCLE_ or MAFFT_. Gap2Seq_ is used to seal gaps between scaffolded *de novo* contigs with sequencing reads.

Expand All @@ -51,7 +50,6 @@ reads were changed to N.

This align-call-refine cycle is iterated twice, to minimize reference bias in the assembly.

.. _Trinity: http://trinityrnaseq.github.io/
.. _SPAdes: http://bioinf.spbau.ru/en/spades
.. _MUMMER: https://mummer4.github.io/
.. _MUSCLE: https://www.drive5.com/muscle/
Expand Down
40 changes: 3 additions & 37 deletions pipes/WDL/tasks/tasks_assembly.wdl
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Expand Up @@ -5,11 +5,10 @@ task assemble {
File reads_unmapped_bam
File trim_clip_db

Int? trinity_n_reads=250000
Int? spades_n_reads=10000000
Int? spades_min_contig_len=0

String? assembler="trinity" # trinity, spades, or trinity-spades
String? assembler="spades"
Boolean? always_succeed=false

# do this in two steps in case the input doesn't actually have "taxfilt" in the name
Expand All @@ -28,18 +27,7 @@ task assemble {

assembly.py --version | tee VERSION

if [[ "${assembler}" == "trinity" ]]; then
assembly.py assemble_trinity \
${reads_unmapped_bam} \
${trim_clip_db} \
${sample_name}.assembly1-${assembler}.fasta \
${'--n_reads=' + trinity_n_reads} \
${true='--alwaysSucceed' false="" always_succeed} \
--JVMmemory "$mem_in_mb"m \
--outReads=${sample_name}.subsamp.bam \
--loglevel=DEBUG

elif [[ "${assembler}" == "spades" ]]; then
if [[ "${assembler}" == "spades" ]]; then
assembly.py assemble_spades \
${reads_unmapped_bam} \
${trim_clip_db} \
Expand All @@ -50,28 +38,6 @@ task assemble {
--memLimitGb $mem_in_gb \
--outReads=${sample_name}.subsamp.bam \
--loglevel=DEBUG

elif [[ "${assembler}" == "trinity-spades" ]]; then
assembly.py assemble_trinity \
${reads_unmapped_bam} \
${trim_clip_db} \
${sample_name}.assembly1-trinity.fasta \
${'--n_reads=' + trinity_n_reads} \
--JVMmemory "$mem_in_mb"m \
--outReads=${sample_name}.subsamp.bam \
${true='--always_succeed' false='' always_succeed} \
--loglevel=DEBUG
assembly.py assemble_spades \
${reads_unmapped_bam} \
${trim_clip_db} \
${sample_name}.assembly1-${assembler}.fasta \
--contigsUntrusted=${sample_name}.assembly1-trinity.fasta \
${'--nReads=' + spades_n_reads} \
${true='--alwaysSucceed' false='' always_succeed} \
${'--minContigLen=' + spades_min_contig_len} \
--memLimitGb $mem_in_gb \
--loglevel=DEBUG

else
echo "unrecognized assembler ${assembler}" >&2
exit 1
Expand Down Expand Up @@ -117,7 +83,7 @@ task scaffold {
String docker="quay.io/broadinstitute/viral-assemble:2.1.4.0"

# do this in multiple steps in case the input doesn't actually have "assembly1-x" in the name
String sample_name = basename(basename(basename(contigs_fasta, ".fasta"), ".assembly1-trinity"), ".assembly1-spades")
String sample_name = basename(basename(contigs_fasta, ".fasta"), ".assembly1-spades")
}

command {
Expand Down