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per-sample reference and sra-ftp utilities #148

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per-sample reference and sra-ftp utilities #148

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@bluegenes bluegenes commented May 13, 2019 •
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  • enable per-sample reference (specify in tsv)
  • enable SRA link generation from SRR number

bluegenes added 30 commits April 4, 2019 15:10
@bluegenes
name outputs
b294c9e
@bluegenes
get output names from included rules
7fd5c78
@bluegenes
init different check_inputs
e9860e7
@bluegenes
Merge branch 'master' into check_inputs
53ca02e
@bluegenes
saving in progress changes
1573cd2
@bluegenes
upd fastqc
4ba6567
@bluegenes
Merge branch 'master' into check_inputs
d5e656a
@bluegenes
saving in progress work
718f37b
@bluegenes
more progress on output_options
b2fc0f6
@bluegenes
closer..
a4e5c35
@bluegenes
handle unutilized keys in config yaml
7a6f430
@bluegenes
all preprocess working
85590d9
@bluegenes
write available extensions in utils
5b31edb
@bluegenes
handle _any_ param as input option
2758789
@bluegenes
upd salmon
71d45fd
@bluegenes
upd sourmash params
8fc4b27
@bluegenes
upd paladin params
a503902
@bluegenes
upd paladin
ddadb41
@bluegenes
fix salmon
a82459f
@bluegenes
upd plass
1f66352
@bluegenes
upd se quantify
99c0544
@bluegenes
upd deseq2 params
f483a5f
@bluegenes
init sra link generation
630c3b6
@bluegenes
finish sra link code
3d661e7
@bluegenes
init per-sample assemblies
143b1d6
@bluegenes
a bit towards per-sample assemblies
83d12f9
@bluegenes
add localrules
af4914b
@bluegenes
saving in-progress per-sample ref changes
5a34bfe
@bluegenes
rm mkdocs files
0dea1bf
@bluegenes
go back to submodule
5bace6b
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@bluegenes