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Merge pull request #59 from wtsi-npg/devel
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post-process md5 sum output
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dozy committed Nov 21, 2014
2 parents 4999234 + 5e487b7 commit 24b821d
Showing 1 changed file with 14 additions and 1 deletion.
15 changes: 14 additions & 1 deletion data/vtlib/final_output_prep.json
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
"outputs":{
"_stdout_":"bamrecompress",
"out_cram":"scramble_tee:__CRAM_OUT__",
"out_cram_md5":"scramble_md5",
"out_cram_md5":"postprocess_md5",
"out_bamcheck":"bamcheck",
"out_stats_F0x900":"samtools_stats_F0x900",
"out_stats_F0xB00":"samtools_stats_F0xB00",
Expand Down Expand Up @@ -131,6 +131,14 @@
"use_STDOUT": true,
"cmd":"md5sum"
},
{
"id":"postprocess_md5",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": true,
"cmd":["tr", "-d", " \\-\n"],
"comment":"the double-backslash is required to get the correct character set to the tr command"
},
{
"id":"bamcheck",
"type":"EXEC",
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"from":"scramble_tee:__MD5_OUT__",
"to":"scramble_md5"
},
{
"id":"md5_to_postprocess",
"from":"scramble_md5",
"to":"postprocess_md5"
},
{
"id":"bmd_to_bamcheck",
"from":"bmd_multiway:__BAMCHECK_OUT__",
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