From 18484f8cea274dbc02a0800c3bed2c52391142d8 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Thu, 6 Jul 2023 17:09:09 +0000 Subject: [PATCH 01/12] update nextclade parsing for latest dataset tag --- tasks/taxon_id/task_nextclade.wdl | 56 ++++++++++++++----------------- 1 file changed, 25 insertions(+), 31 deletions(-) diff --git a/tasks/taxon_id/task_nextclade.wdl b/tasks/taxon_id/task_nextclade.wdl index 375617965..98c30de43 100644 --- a/tasks/taxon_id/task_nextclade.wdl +++ b/tasks/taxon_id/task_nextclade.wdl @@ -91,45 +91,43 @@ task nextclade_output_parser { tamiflu_aa_subs = tamiflu_aa_subs + "~{tamiflu_aa_substitutions}".split(',') - print(tamiflu_aa_subs) - def intersection(lst1, lst2): # returns intersection between nextclade identified aa substitutions and # tamiflu associated aa substitutions return list(set(lst1) & set(lst2)) with codecs.open("./input.tsv",'r') as tsv_file: - tsv_reader=csv.reader(tsv_file, delimiter="\t") - tsv_data=list(tsv_reader) + tsv_reader = csv.reader(tsv_file, delimiter="\t") + tsv_data = list(tsv_reader) - if len(tsv_data)==1: + if len(tsv_data) == 1: tsv_data.append(['NA']*len(tsv_data[0])) - tsv_dict=dict(zip(tsv_data[0], tsv_data[1])) + tsv_dict = dict(zip(tsv_data[0], tsv_data[1])) - # parse 'clade_legacy' column if sars-cov-2, if false then parse 'clade' column + # combine 'clade_nextstrain' and 'clade_who' column if sars-cov-2, if false then parse 'clade' column if ("~{organism}" == "sars-cov-2"): with codecs.open("NEXTCLADE_CLADE", 'wt') as Nextclade_Clade: - nc_clade=tsv_dict['clade_legacy'] - if nc_clade=='': - nc_clade='NA' - else: - nc_clade=nc_clade + nextstrain_clade = tsv_dict['clade_nextstrain'] + who_clade = tsv_dict['clade_who'] + if nextclade_clade != who_clade: + nc_clade = nextclade_clade + " (" + who_clade + ")" + if nc_clade == '': + nc_clade = 'NA' + else: # in the case where both are "recombinant," only print the first + nc_clade = nextclade_clade Nextclade_Clade.write(nc_clade) else: with codecs.open("NEXTCLADE_CLADE", 'wt') as Nextclade_Clade: - nc_clade=tsv_dict['clade'] - if nc_clade=='': - nc_clade='NA' - else: - nc_clade=nc_clade + nc_clade = tsv_dict['clade'] + if nc_clade == '': + nc_clade = 'NA' Nextclade_Clade.write(nc_clade) with codecs.open("NEXTCLADE_AASUBS", 'wt') as Nextclade_AA_Subs: - nc_aa_subs=tsv_dict['aaSubstitutions'] - if nc_aa_subs=='': - nc_aa_subs='NA' + nc_aa_subs = tsv_dict['aaSubstitutions'] + if nc_aa_subs == '': + nc_aa_subs = 'NA' else: - nc_aa_subs=nc_aa_subs # if organism is flu, return list of aa subs associated with tamiflu resistance if ("~{organism}" == "flu" and "~{NA_segment}" == "true"): tamiflu_subs = intersection(tamiflu_aa_subs, nc_aa_subs.split(',')) @@ -138,22 +136,18 @@ task nextclade_output_parser { Nextclade_AA_Subs.write(nc_aa_subs) with codecs.open("NEXTCLADE_AADELS", 'wt') as Nextclade_AA_Dels: - nc_aa_dels=tsv_dict['aaDeletions'] - if nc_aa_dels=='': - nc_aa_dels='NA' - else: - nc_aa_dels=nc_aa_dels + nc_aa_dels = tsv_dict['aaDeletions'] + if nc_aa_dels == '': + nc_aa_dels = 'NA' Nextclade_AA_Dels.write(nc_aa_dels) with codecs.open("NEXTCLADE_LINEAGE", 'wt') as Nextclade_Lineage: if 'lineage' in tsv_dict: - nc_lineage=tsv_dict['lineage'] + nc_lineage = tsv_dict['lineage'] if nc_lineage is None: - nc_lineage="" - else: - nc_lineage=nc_lineage + nc_lineage = "" else: - nc_lineage="" + nc_lineage = "" Nextclade_Lineage.write(nc_lineage) CODE >>> From 3d8d5c22583970043d343ca9d1c536bc07d4087e Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Thu, 6 Jul 2023 17:29:58 +0000 Subject: [PATCH 02/12] fix variable name --- tasks/taxon_id/task_nextclade.wdl | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/tasks/taxon_id/task_nextclade.wdl b/tasks/taxon_id/task_nextclade.wdl index 98c30de43..d0c2fb191 100644 --- a/tasks/taxon_id/task_nextclade.wdl +++ b/tasks/taxon_id/task_nextclade.wdl @@ -107,14 +107,12 @@ task nextclade_output_parser { # combine 'clade_nextstrain' and 'clade_who' column if sars-cov-2, if false then parse 'clade' column if ("~{organism}" == "sars-cov-2"): with codecs.open("NEXTCLADE_CLADE", 'wt') as Nextclade_Clade: - nextstrain_clade = tsv_dict['clade_nextstrain'] + nc_clade = tsv_dict['clade_nextstrain'] who_clade = tsv_dict['clade_who'] - if nextclade_clade != who_clade: - nc_clade = nextclade_clade + " (" + who_clade + ")" - if nc_clade == '': - nc_clade = 'NA' - else: # in the case where both are "recombinant," only print the first - nc_clade = nextclade_clade + if nc_clade != who_clade: + nc_clade = nc_clade + " (" + who_clade + ")" + if nc_clade == '': + nc_clade = 'NA' Nextclade_Clade.write(nc_clade) else: with codecs.open("NEXTCLADE_CLADE", 'wt') as Nextclade_Clade: From 0f3a5fd9a22eccac7bd31affdea966d73aa174e5 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Thu, 6 Jul 2023 17:31:39 +0000 Subject: [PATCH 03/12] fix logic --- tasks/taxon_id/task_nextclade.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/taxon_id/task_nextclade.wdl b/tasks/taxon_id/task_nextclade.wdl index d0c2fb191..680852376 100644 --- a/tasks/taxon_id/task_nextclade.wdl +++ b/tasks/taxon_id/task_nextclade.wdl @@ -109,7 +109,7 @@ task nextclade_output_parser { with codecs.open("NEXTCLADE_CLADE", 'wt') as Nextclade_Clade: nc_clade = tsv_dict['clade_nextstrain'] who_clade = tsv_dict['clade_who'] - if nc_clade != who_clade: + if (nc_clade != who_clade) and (nc_clade != ''): nc_clade = nc_clade + " (" + who_clade + ")" if nc_clade == '': nc_clade = 'NA' From 1aeb16a4e02aca960750b65356dfb084348a9fe5 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Thu, 6 Jul 2023 17:46:44 +0000 Subject: [PATCH 04/12] logic tweak --- tasks/taxon_id/task_nextclade.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/taxon_id/task_nextclade.wdl b/tasks/taxon_id/task_nextclade.wdl index 680852376..9786cb4d9 100644 --- a/tasks/taxon_id/task_nextclade.wdl +++ b/tasks/taxon_id/task_nextclade.wdl @@ -109,7 +109,7 @@ task nextclade_output_parser { with codecs.open("NEXTCLADE_CLADE", 'wt') as Nextclade_Clade: nc_clade = tsv_dict['clade_nextstrain'] who_clade = tsv_dict['clade_who'] - if (nc_clade != who_clade) and (nc_clade != ''): + if (nc_clade != who_clade) and (nc_clade != '') and (who_clade != ''): nc_clade = nc_clade + " (" + who_clade + ")" if nc_clade == '': nc_clade = 'NA' From a924dd7cb141bd207360ab6c2df3e0cc3291325c Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Thu, 6 Jul 2023 18:03:10 +0000 Subject: [PATCH 05/12] please stop failing --- tasks/phylogenetic_inference/task_lyveset.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/phylogenetic_inference/task_lyveset.wdl b/tasks/phylogenetic_inference/task_lyveset.wdl index 089d34d3f..2d45bc660 100644 --- a/tasks/phylogenetic_inference/task_lyveset.wdl +++ b/tasks/phylogenetic_inference/task_lyveset.wdl @@ -6,7 +6,7 @@ task lyveset { Array[File] read2 File reference_genome String dataset_name - String docker_image = "quay.io/staphb/lyveset:1.1.4f" + String docker_image = "staphb/lyveset:1.1.4f" Int memory = 64 Int cpu = 16 Int disk_size = 100 From 7d8ff1efe32f85f512d8b2423a644559a9bd3b1a Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Thu, 6 Jul 2023 18:23:13 +0000 Subject: [PATCH 06/12] update md5sums --- tests/config/pytest_filter.yml | 4 ---- tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml | 4 ++-- tests/workflows/theiacov/test_wf_theiacov_fasta.yml | 4 ++-- tests/workflows/theiacov/test_wf_theiacov_ont.yml | 4 ++-- 4 files changed, 6 insertions(+), 10 deletions(-) diff --git a/tests/config/pytest_filter.yml b/tests/config/pytest_filter.yml index f245df41a..be17ab072 100644 --- a/tests/config/pytest_filter.yml +++ b/tests/config/pytest_filter.yml @@ -75,10 +75,6 @@ wf_theiacov_ont: - tasks/gene_typing/task_sc2_gene_coverage.wdl - tasks/task_versioning.wdl -wf_theiacov_validate: - - tasks/utilities/task_validate.wdl - - tasks/task_versioning.wdl - wf_theiaprok_illumina_pe: - workflows/theiaprok/wf_theiaprok_illumina_pe.wdl - tasks/assembly/task_shovill.wdl diff --git a/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml b/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml index 5f28da123..df60774cb 100644 --- a/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml +++ b/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml @@ -226,7 +226,7 @@ - path: miniwdl_run/call-nextclade/work/NEXTCLADE_VERSION md5sum: d5f4e83525024cba7eb7489cd5209e7d - path: miniwdl_run/call-nextclade/work/_miniwdl_inputs/0/clearlabs.medaka.consensus.fasta - md5sum: d41d8cd98f00b204e9800998ecf8427e + md5sum: 91a455762183b41af0d8de5596e28e7f - path: miniwdl_run/call-nextclade/work/clearlabs.medaka.consensus.nextclade.auspice.json - path: miniwdl_run/call-nextclade/work/clearlabs.medaka.consensus.nextclade.json - path: miniwdl_run/call-nextclade/work/clearlabs.medaka.consensus.nextclade.tsv @@ -276,7 +276,7 @@ - path: miniwdl_run/call-nextclade/work/nextclade_gene_S.translation.fasta md5sum: 0ce44a0a8e2784ca4b3e8d8f03211813 - path: miniwdl_run/call-nextclade_output_parser/command - md5sum: 15e4d72fff3a4e2b81ce30a4668266f0 + md5sum: 8bab8bc62cb16fff613907f34c54ec51 - path: miniwdl_run/call-nextclade_output_parser/inputs.json contains: ["nextclade_tsv", "tsv"] - path: miniwdl_run/call-nextclade_output_parser/outputs.json diff --git a/tests/workflows/theiacov/test_wf_theiacov_fasta.yml b/tests/workflows/theiacov/test_wf_theiacov_fasta.yml index 20103f92a..4f244fe50 100644 --- a/tests/workflows/theiacov/test_wf_theiacov_fasta.yml +++ b/tests/workflows/theiacov/test_wf_theiacov_fasta.yml @@ -46,7 +46,7 @@ - path: miniwdl_run/call-nextclade/stdout.txt - path: miniwdl_run/call-nextclade/task.log - path: miniwdl_run/call-nextclade/work/NEXTCLADE_VERSION - md5sum: d5f4e83525024cba7eb7489cd5209e7d + md5sum: 91a455762183b41af0d8de5596e28e7f - path: miniwdl_run/call-nextclade/work/_miniwdl_inputs/0/clearlabs.fasta.gz - path: miniwdl_run/call-nextclade/work/clearlabs.fasta.gz.nextclade.auspice.json - path: miniwdl_run/call-nextclade/work/clearlabs.fasta.gz.nextclade.json @@ -100,7 +100,7 @@ - path: miniwdl_run/call-nextclade/work/nextclade_gene_S.translation.fasta md5sum: e630a638abbb2c8ab4a8b74455e9668f - path: miniwdl_run/call-nextclade_output_parser/command - md5sum: 632edfc9ac20d8134d3e22f507de1e08 + md5sum: 8bab8bc62cb16fff613907f34c54ec51 - path: miniwdl_run/call-nextclade_output_parser/inputs.json - path: miniwdl_run/call-nextclade_output_parser/outputs.json - path: miniwdl_run/call-nextclade_output_parser/stderr.txt diff --git a/tests/workflows/theiacov/test_wf_theiacov_ont.yml b/tests/workflows/theiacov/test_wf_theiacov_ont.yml index e2177e38d..6d43faa64 100644 --- a/tests/workflows/theiacov/test_wf_theiacov_ont.yml +++ b/tests/workflows/theiacov/test_wf_theiacov_ont.yml @@ -235,7 +235,7 @@ - path: miniwdl_run/call-nextclade/task.log contains: ["wdl", "theiacov_ont", "done"] - path: miniwdl_run/call-nextclade/work/NEXTCLADE_VERSION - md5sum: d5f4e83525024cba7eb7489cd5209e7d + md5sum: 91a455762183b41af0d8de5596e28e7f - path: miniwdl_run/call-nextclade/work/_miniwdl_inputs/0/ont.medaka.consensus.fasta md5sum: d41d8cd98f00b204e9800998ecf8427e - path: miniwdl_run/call-nextclade/work/nextclade.aligned.fasta @@ -285,7 +285,7 @@ - path: miniwdl_run/call-nextclade/work/ont.medaka.consensus.nextclade.json - path: miniwdl_run/call-nextclade/work/ont.medaka.consensus.nextclade.tsv - path: miniwdl_run/call-nextclade_output_parser/command - md5sum: 65e8a95529a0466257beed44ec71d2ca + md5sum: 8bab8bc62cb16fff613907f34c54ec51 - path: miniwdl_run/call-nextclade_output_parser/inputs.json contains: ["nextclade_tsv", "tsv"] - path: miniwdl_run/call-nextclade_output_parser/outputs.json From a68b09e7ed7100f90af660f41c87e0f474566467 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Thu, 6 Jul 2023 18:56:10 +0000 Subject: [PATCH 07/12] potential fix --- .github/workflows/pytest-workflows.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/pytest-workflows.yml b/.github/workflows/pytest-workflows.yml index 6c72196f4..47683b3a6 100644 --- a/.github/workflows/pytest-workflows.yml +++ b/.github/workflows/pytest-workflows.yml @@ -6,6 +6,9 @@ name: Pytest Workflows on: push: + # remove this section once the miniwdl test is reinstated for TheiaCoV_Illumina_PE/_SE + paths-ignore: + - 'workflows/theiacov/theiacov_illumina_**' branches: [main] pull_request: branches: [main] From 92c399f4cedb642c2cf1d2ee1b1baba0dfe604f8 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Thu, 6 Jul 2023 19:09:42 +0000 Subject: [PATCH 08/12] another attempt --- .github/workflows/pytest-workflows.yml | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/.github/workflows/pytest-workflows.yml b/.github/workflows/pytest-workflows.yml index 47683b3a6..aacf09b0c 100644 --- a/.github/workflows/pytest-workflows.yml +++ b/.github/workflows/pytest-workflows.yml @@ -6,9 +6,6 @@ name: Pytest Workflows on: push: - # remove this section once the miniwdl test is reinstated for TheiaCoV_Illumina_PE/_SE - paths-ignore: - - 'workflows/theiacov/theiacov_illumina_**' branches: [main] pull_request: branches: [main] @@ -41,6 +38,11 @@ jobs: # For every workflow, test it with MiniWDL and Cromwell tag: ["${{ fromJson(needs.changes.outputs.workflows) }}"] engine: ["miniwdl", "cromwell"] + exclude: + - tag: wf_theiacov_illumina_pe + engine: miniwdl + - tag: wf_theiacov_illumina_se + engine: miniwdl defaults: run: # Play nicely with miniconda @@ -65,14 +67,10 @@ jobs: auto-activate-base: false # Depends and env info (mostly for debug) - # rm -rf commands as recommended here: https://github.com/actions/runner-images/issues/2840#issuecomment-1284059930 - - name: Install Dependencies and create storage space + - name: Install Dependencies run: | conda install -y -c conda-forge -c bioconda cromwell miniwdl=1.5.2 'python>=3.7' pytest pytest-workflow 'importlib-metadata<=4.13.0' - conda clean -a -y uname -a && env - sudo rm -rf /usr/share/dotnet - sudo rm -rf "$AGENT_TOOLSDIRECTORY" - name: Test ${{ matrix.tag }} run: TMPDIR=~ pytest --tag ${{ matrix.tag }}_${{ matrix.engine }} --symlink --kwdof --color=yes From bef425b2eb65dd0ca2e8bec8cdc8366cfe23fad1 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Thu, 6 Jul 2023 19:13:37 +0000 Subject: [PATCH 09/12] trying quotations --- .github/workflows/pytest-workflows.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pytest-workflows.yml b/.github/workflows/pytest-workflows.yml index aacf09b0c..7f0fd859f 100644 --- a/.github/workflows/pytest-workflows.yml +++ b/.github/workflows/pytest-workflows.yml @@ -39,10 +39,10 @@ jobs: tag: ["${{ fromJson(needs.changes.outputs.workflows) }}"] engine: ["miniwdl", "cromwell"] exclude: - - tag: wf_theiacov_illumina_pe - engine: miniwdl - - tag: wf_theiacov_illumina_se - engine: miniwdl + - tag: "wf_theiacov_illumina_pe" + engine: "miniwdl" + - tag: "wf_theiacov_illumina_se" + engine: "miniwdl" defaults: run: # Play nicely with miniconda From adc94bf65e4f1178be5b078d5563b74d2f7d7bea Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Fri, 7 Jul 2023 13:16:36 +0000 Subject: [PATCH 10/12] create storage space, thanks curtis --- .github/workflows/pytest-workflows.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pytest-workflows.yml b/.github/workflows/pytest-workflows.yml index 7f0fd859f..a6b2cb404 100644 --- a/.github/workflows/pytest-workflows.yml +++ b/.github/workflows/pytest-workflows.yml @@ -67,10 +67,14 @@ jobs: auto-activate-base: false # Depends and env info (mostly for debug) - - name: Install Dependencies + # rm -rf commands as recommended here: https://github.com/actions/runner-images/issues/2840#issuecomment-1284059930 + - name: Install Dependencies and create storage space run: | conda install -y -c conda-forge -c bioconda cromwell miniwdl=1.5.2 'python>=3.7' pytest pytest-workflow 'importlib-metadata<=4.13.0' + conda clean -a -y uname -a && env + sudo rm -rf /usr/share/dotnet + sudo rm -rf "$AGENT_TOOLSDIRECTORY" - name: Test ${{ matrix.tag }} run: TMPDIR=~ pytest --tag ${{ matrix.tag }}_${{ matrix.engine }} --symlink --kwdof --color=yes From 28f5d31df290ee4a05e3513ea4b4f6bb380f0bba Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Fri, 7 Jul 2023 13:37:41 +0000 Subject: [PATCH 11/12] update md5sums --- tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml | 6 +++--- tests/workflows/theiacov/test_wf_theiacov_ont.yml | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml b/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml index df60774cb..b7fe471c3 100644 --- a/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml +++ b/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml @@ -224,9 +224,9 @@ - path: miniwdl_run/call-nextclade/task.log contains: ["wdl", "theiacov_clearlabs", "nextclade", "done"] - path: miniwdl_run/call-nextclade/work/NEXTCLADE_VERSION - md5sum: d5f4e83525024cba7eb7489cd5209e7d - - path: miniwdl_run/call-nextclade/work/_miniwdl_inputs/0/clearlabs.medaka.consensus.fasta md5sum: 91a455762183b41af0d8de5596e28e7f + - path: miniwdl_run/call-nextclade/work/_miniwdl_inputs/0/clearlabs.medaka.consensus.fasta + md5sum: d41d8cd98f00b204e9800998ecf8427e - path: miniwdl_run/call-nextclade/work/clearlabs.medaka.consensus.nextclade.auspice.json - path: miniwdl_run/call-nextclade/work/clearlabs.medaka.consensus.nextclade.json - path: miniwdl_run/call-nextclade/work/clearlabs.medaka.consensus.nextclade.tsv @@ -276,7 +276,7 @@ - path: miniwdl_run/call-nextclade/work/nextclade_gene_S.translation.fasta md5sum: 0ce44a0a8e2784ca4b3e8d8f03211813 - path: miniwdl_run/call-nextclade_output_parser/command - md5sum: 8bab8bc62cb16fff613907f34c54ec51 + md5sum: a01b0a826425399bc59854b7c74acb1e - path: miniwdl_run/call-nextclade_output_parser/inputs.json contains: ["nextclade_tsv", "tsv"] - path: miniwdl_run/call-nextclade_output_parser/outputs.json diff --git a/tests/workflows/theiacov/test_wf_theiacov_ont.yml b/tests/workflows/theiacov/test_wf_theiacov_ont.yml index 6d43faa64..9982b01ff 100644 --- a/tests/workflows/theiacov/test_wf_theiacov_ont.yml +++ b/tests/workflows/theiacov/test_wf_theiacov_ont.yml @@ -285,7 +285,7 @@ - path: miniwdl_run/call-nextclade/work/ont.medaka.consensus.nextclade.json - path: miniwdl_run/call-nextclade/work/ont.medaka.consensus.nextclade.tsv - path: miniwdl_run/call-nextclade_output_parser/command - md5sum: 8bab8bc62cb16fff613907f34c54ec51 + md5sum: 5354c0f11f6f2301ce6f0a07dc3b3aca - path: miniwdl_run/call-nextclade_output_parser/inputs.json contains: ["nextclade_tsv", "tsv"] - path: miniwdl_run/call-nextclade_output_parser/outputs.json From 1ede00c929852a79a00697187c5346ff131730e6 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Thu, 13 Jul 2023 16:17:01 +0000 Subject: [PATCH 12/12] convert decimals to dashes too --- workflows/utilities/data_import/wf_basespace_fetch.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/utilities/data_import/wf_basespace_fetch.wdl b/workflows/utilities/data_import/wf_basespace_fetch.wdl index 71c0fcfe3..650211eb3 100644 --- a/workflows/utilities/data_import/wf_basespace_fetch.wdl +++ b/workflows/utilities/data_import/wf_basespace_fetch.wdl @@ -99,7 +99,7 @@ task fetch_bs { # rename FASTQ files to add back in underscores that Illumina/Basespace changed into hyphens echo "Concatenating and renaming FASTQ files to add back underscores in basespace_sample_name" # setting a new bash variable to use for renaming during concatenation of FASTQs - SAMPLENAME_HYPHEN_INSTEAD_OF_UNDERSCORES=$(echo $sample_identifier | sed 's|_|-|g') + SAMPLENAME_HYPHEN_INSTEAD_OF_UNDERSCORES=$(echo $sample_identifier | sed 's|_|-|g' | sed 's|\.|-|g') #Combine non-empty read files into single file without BaseSpace filename cruft ##FWD Read