Merge pull request #366 from broadinstitute/dp-biosample

dpark01 · web-flow · commit 360cf33068e7 · 2021-09-24T08:56:56.000-04:00
rework biosample_load to not use todays date in ftp directory path
diff --git a/pipes/WDL/workflows/sarscov2_biosample_load.wdl b/pipes/WDL/workflows/sarscov2_biosample_load.wdl
@@ -32,7 +32,6 @@ workflow sarscov2_biosample_load {
 
     File meta_submit_tsv = select_first([biosample_submit_tsv, crsp_meta_etl.biosample_submit_tsv])
 
-    call utils.today
     call utils.md5sum {
         input:
             in_file = meta_submit_tsv
@@ -51,7 +50,7 @@ workflow sarscov2_biosample_load {
             input:
                 meta_submit_tsv = biosample_tsv_filter_preexisting.meta_unsubmitted_tsv,
                 config_js = ftp_config_js,
-                target_path = "/~{prod_test}/~{today.date}_~{md5sum.md5}/biosample"
+                target_path = "/~{prod_test}/biosample/~{basename(meta_submit_tsv, '.tsv')}/~{md5sum.md5}"
         }
     }
 

Original file line number	Diff line number	Diff line change
`@@ -32,7 +32,6 @@ workflow sarscov2_biosample_load {`
`32`	`32`
`33`	`33`	`File meta_submit_tsv = select_first([biosample_submit_tsv, crsp_meta_etl.biosample_submit_tsv])`
`34`	`34`
`35`		`- call utils.today`
`36`	`35`	`call utils.md5sum {`
`37`	`36`	`input:`
`38`	`37`	`in_file = meta_submit_tsv`
`@@ -51,7 +50,7 @@ workflow sarscov2_biosample_load {`
`51`	`50`	`input:`
`52`	`51`	`meta_submit_tsv = biosample_tsv_filter_preexisting.meta_unsubmitted_tsv,`
`53`	`52`	`config_js = ftp_config_js,`
`54`		`- target_path = "/~{prod_test}/~{today.date}_~{md5sum.md5}/biosample"`
	`53`	`+ target_path = "/~{prod_test}/biosample/~{basename(meta_submit_tsv, '.tsv')}/~{md5sum.md5}"`
`55`	`54`	`}`
`56`	`55`	`}`
`57`	`56`