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Pathogens changes #40

Merged
merged 327 commits into from Jun 14, 2012
Merged

Pathogens changes #40

merged 327 commits into from Jun 14, 2012

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andrewjpage
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@andrewjpage
cleanup step
c8aff95
@andrewjpage
missing semicolon
2585265
@andrewjpage
optimised with reference directory
793ec6b
@andrewjpage
sspace typos
918c397
@andrewjpage
sspace
f698970
@andrewjpage
merge sizes
3a9476d
@andrewjpage
fix scaffolder exec
6bce313
@andrewjpage
create config file
67a8d88
@andrewjpage
config file array files
7e0c944
@andrewjpage
scaffolder names different to expected
bec6a20
@andrewjpage
dont error when making directory
1dbf8fc
@andrewjpage
more scaffolding
5027560
@andrewjpage
fix the output file from the scaffolding step
4c5273f
@andrewjpage
dont delete forward and reverse fastqs
96f948b
@andrewjpage
increase mapping ram
c7a9e89
@andrewjpage
increase scale on bamcheck graphs
e7d7b5f
@andrewjpage
Merge branch 'assembly' into pipeline
7ef6211
@andrewjpage
Merge pull request #39 from andrewjpage/pipeline
8e782dc 
Assembly pipeline
@andrewjpage
cleanup assembly files
56e2f88
@andrewjpage
add assembled processed flag
a7ab4b7
@andrewjpage
allow a user to provide a reference to guide an assembly
069a89a
@andrewjpage
declare reference
466a654
@andrewjpage
Merge pull request #40 from andrewjpage/user_provided_reference
bfdbdf7 
User provided reference
@andrewjpage
only use reference when using columbus
638189e
@andrewjpage
run cleanup
be50b81
@andrewjpage
Merge pull request #41 from andrewjpage/only_use_ref_for_columbus
d7029d2 
Only use ref for columbus
@andrewjpage
better adjusting of memory limits
3bae0fe
@andrewjpage
Merge pull request #42 from andrewjpage/only_use_ref_for_columbus
813afec 
better adjusting of memory limits
@andrewjpage
when tag changes choose current aliquot
beb33ca
@andrewjpage
Merge pull request #43 from andrewjpage/choose_current_aliquot_multip…
7d6c834 
…lexed_library

when tag changes choose current aliquot
@andrewjpage
lookup filenames for assembly pipeline
7779dea
@andrewjpage
Merge pull request #93 from andrewjpage/assembly_pipeline_external_data
75454c5 
lookup filenames for assembly pipeline
@andrewjpage
use correct filename varable
1f11b19
@andrewjpage
Merge pull request #94 from andrewjpage/assembly_pipeline_external_data
8db68f9 
use correct filename varable
@andrewjpage
filenames as array ref
9ef979b
@andrewjpage
Merge pull request #95 from andrewjpage/assembly_pipeline_external_data
23c2c3a 
filenames as array ref
@andrewjpage
filenames as array ref
489434a
@andrewjpage
Merge pull request #96 from andrewjpage/assembly_pipeline_external_data
e7d14f2 
filenames as array ref
@andrewjpage
search for fastq files
1e02d09
@andrewjpage
construct fastq file name
af6677c
@andrewjpage
Merge pull request #97 from andrewjpage/assembly_pipeline_external_data
73aac3d 
Assembly pipeline external data
@andrewjpage
remove util cmd
630eaa0
@andrewjpage
Merge pull request #98 from andrewjpage/pipeline
a1b169b 
remove util cmd
@andrewjpage
use pipelines mapping
4a878ba
@andrewjpage
Merge pull request #99 from andrewjpage/pipeline
e647ebb 
use pipelines mapping
@andrewjpage
increase merge mapping memory and delete intermediate tmp file if found
8d15cdf
@andrewjpage
Merge pull request #100 from andrewjpage/mapping_merge_memory
ea678e0 
increase merge mapping memory and delete intermediate tmp file if found
@andrewjpage
dont set a bad run status if tmp file is initially deleted
c5b7996
@andrewjpage
Merge pull request #101 from andrewjpage/mapping_merge_memory
baa5876 
dont set a bad run status if tmp file is initially deleted
@andrewjpage
delete intermediate file produced by merging with samtools
a92cc4e
@andrewjpage
Merge pull request #102 from andrewjpage/mapping_merge_memory
c7c7a6b 
delete intermediate file produced by merging with samtools
@andrewjpage
increase minimum velvet memory to 6gb
0a8bde4
@andrewjpage
Merge pull request #103 from andrewjpage/increase_min_velvet_memory
eb38d86 
increase minimum velvet memory to 6gb
@andrewjpage
Merge branch 'develop' of http://github.com/VertebrateResequencing/vr…
1dc4381 
…-codebase into pipeline
@andrewjpage
declare bam name
13ac90a
@andrewjpage
Merge pull request #105 from andrewjpage/name_in_trackqc_bam
6ce27f0 
Name in trackqc bam
@andrewjpage
pass in insert size to fastq qc method
dd96ba0
@andrewjpage
Merge pull request #106 from andrewjpage/name_in_trackqc_bam
b391a2b 
pass in insert size to fastq qc method
sb10 added a commit that referenced this pull request Jun 14, 2012
@sb10
Merge pull request #40 from sanger-pathogens/pipeline
ccc1ca9 
Pathogens changes
@sb10 sb10 merged commit ccc1ca9 into VertebrateResequencing:develop Jun 14, 2012
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4 participants
@andrewjpage @sb10 @CraigPorter @aslett1