I have a WDL task that ran in FC today.
The task has some inputs. Two of them are described here. One "pcovs" comes from the user/WDL and is an array of files. The other derived from the first via write_lines. See the snippet:
Array[File] pcovs
File thesePcovs_FOF=write_lines(pcovs)
command <<<
#increase verbosity
set -ex
#set up input to point to the pcovs
echo "To build PON using : "
grep -Pin '.' ${thesePcovs_FOF}
the snippet was run with the array of files passed from a scatter also of width 2. The two files were listed in the inputs sections (revealed after clicking "Show") and are copied/pasted here : (["gs://fc-e98be011-00c7-4d5e-8176-58deb8876b4c/39fb8cec-078d-42cc-ae4c-9b12a36915f4/make_acnv_pon_wf/61627692-2877-48de-bf2d-01bfb988d067/call-gatk_cov_pull/shard-0/HCC1143_Normal_WE.coverage.tsv" "gs://fc-e98be011-00c7-4d5e-8176-58deb8876b4c/39fb8cec-078d-42cc-ae4c-9b12a36915f4/make_acnv_pon_wf/61627692-2877-48de-bf2d-01bfb988d067/call-gatk_cov_pull/shard-1/HCC1954_Normal_100_gene.coverage.tsv"]) . the two files were successfully localized (as shown in the log) :
2017/07/11 14:23:52 I: Running command: sudo gsutil -q -m cp gs://fc-e98be011-00c7-4d5e-8176-58deb8876b4c/39fb8cec-078d-42cc-ae4c-9b12a36915f4/make_acnv_pon_wf/61627692-2877-48de-bf2d-01bfb988d067/call-make_acnv_pon/exec.sh /mnt/local-disk/exec.sh
2017/07/11 14:23:54 I: Docker file /cromwell_root/fc-e98be011-00c7-4d5e-8176-58deb8876b4c/39fb8cec-078d-42cc-ae4c-9b12a36915f4/make_acnv_pon_wf/61627692-2877-48de-bf2d-01bfb988d067/call-gatk_cov_pull/shard-0/HCC1143_Normal_WE.coverage.tsv maps to host location /mnt/local-disk/fc-e98be011-00c7-4d5e-8176-58deb8876b4c/39fb8cec-078d-42cc-ae4c-9b12a36915f4/make_acnv_pon_wf/61627692-2877-48de-bf2d-01bfb988d067/call-gatk_cov_pull/shard-0/HCC1143_Normal_WE.coverage.tsv.
2017/07/11 14:23:54 I: Running command: sudo gsutil -q -m cp gs://fc-e98be011-00c7-4d5e-8176-58deb8876b4c/39fb8cec-078d-42cc-ae4c-9b12a36915f4/make_acnv_pon_wf/61627692-2877-48de-bf2d-01bfb988d067/call-gatk_cov_pull/shard-0/HCC1143_Normal_WE.coverage.tsv /mnt/local-disk/fc-e98be011-00c7-4d5e-8176-58deb8876b4c/39fb8cec-078d-42cc-ae4c-9b12a36915f4/make_acnv_pon_wf/61627692-2877-48de-bf2d-01bfb988d067/call-gatk_cov_pull/shard-0/HCC1143_Normal_WE.coverage.tsv
2017/07/11 14:23:55 I: Docker file /cromwell_root/fc-e98be011-00c7-4d5e-8176-58deb8876b4c/39fb8cec-078d-42cc-ae4c-9b12a36915f4/make_acnv_pon_wf/61627692-2877-48de-bf2d-01bfb988d067/call-gatk_cov_pull/shard-1/HCC1954_Normal_100_gene.coverage.tsv maps to host location /mnt/local-disk/fc-e98be011-00c7-4d5e-8176-58deb8876b4c/39fb8cec-078d-42cc-ae4c-9b12a36915f4/make_acnv_pon_wf/61627692-2877-48de-bf2d-01bfb988d067/call-gatk_cov_pull/shard-1/HCC1954_Normal_100_gene.coverage.tsv.
2017/07/11 14:23:55 I: Running command: sudo gsutil -q -m cp gs://fc-e98be011-00c7-4d5e-8176-58deb8876b4c/39fb8cec-078d-42cc-ae4c-9b12a36915f4/make_acnv_pon_wf/61627692-2877-48de-bf2d-01bfb988d067/call-gatk_cov_pull/shard-1/HCC1954_Normal_100_gene.coverage.tsv /mnt/local-disk/fc-e98be011-00c7-4d5e-8176-58deb8876b4c/39fb8cec-078d-42cc-ae4c-9b12a36915f4/make_acnv_pon_wf/61627692-2877-48de-bf2d-01bfb988d067/call-gatk_cov_pull/shard-1/HCC1954_Normal_100_gene.coverage.tsv
when the WDL runs however, I see the following :
To build PON using :
1:gs://fc-e98be011-00c7-4d5e-8176-58deb8876b4c/39fb8cec-078d-42cc-ae4c-9b12a36915f4/make_acnv_pon_wf/61627692-2877-48de-bf2d-01bfb988d067/call-gatk_cov_pull/shard-0/HCC1143_Normal_WE.coverage.tsv
2:gs://fc-e98be011-00c7-4d5e-8176-58deb8876b4c/39fb8cec-078d-42cc-ae4c-9b12a36915f4/make_acnv_pon_wf/61627692-2877-48de-bf2d-01bfb988d067/call-gatk_cov_pull/shard-1/HCC1954_Normal_100_gene.coverage.tsv
SO, it looks like the write_lines does not reflect the localized paths, but rather the paths/URLS of the files pre-localized. Is the observed behavior of write_lines correct? This ran on FC with cromwell27