Update md5sums for clearlabs in TheiaCoV workflow tests

theiagen · Jan 9, 2025 · f889a13 · f889a13
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commit f889a13
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diff --git a/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml b/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml
@@ -41,7 +41,7 @@
     - path: miniwdl_run/call-consensus/work/clearlabs.alignreport.csv
       md5sum: 3cbc074cd5baefbf594c73ddfd633c8a
     - path: miniwdl_run/call-consensus/work/clearlabs.consensus.fasta
-      md5sum: 536f7643ef165dc7d72ca39e46cd3538
+      md5sum: a4dcfa721272ae95a5e950f3e2d25986
     - path: miniwdl_run/call-consensus/work/clearlabs.coverage_mask.txt
       md5sum: f3d76027b8506a5b1d0f5b1c7e7c8cff
     - path: miniwdl_run/call-consensus/work/clearlabs.fail.vcf
@@ -52,10 +52,10 @@
     - path: miniwdl_run/call-consensus/work/clearlabs.pass.vcf
     - path: miniwdl_run/call-consensus/work/clearlabs.pass.vcf.gz.tbi
     - path: miniwdl_run/call-consensus/work/clearlabs.preconsensus.fasta
-      md5sum: 3279c5ce27628f7a34b3d11232e4de65
+      md5sum: 6401ca1acb69843b55b792754a54e444
     - path: miniwdl_run/call-consensus/work/clearlabs.preconsensus.fasta.fai
     - path: miniwdl_run/call-consensus/work/clearlabs.primers.vcf
-      md5sum: 2121a7dd91771d89b3283da5ff897e04
+      md5sum: 8f60b25110cdf39ce27dd48719566416
     - path: miniwdl_run/call-consensus/work/clearlabs.primersitereport.txt
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-consensus/work/clearlabs.primertrimmed.rg.sorted.bam
@@ -77,15 +77,15 @@
       contains: ["wdl", "theiacov_clearlabs", "consensus_qc", "done"]
     - path: miniwdl_run/call-consensus_qc/work/DATE
     - path: miniwdl_run/call-consensus_qc/work/NUM_ACTG
-      md5sum: b042297eaf71f467789516212e2ca5ac
+      md5sum: 8d7e91afbf4b25d066e0e4ee3f757af1
     - path: miniwdl_run/call-consensus_qc/work/NUM_DEGENERATE
       md5sum: 897316929176464ebc9ad085f31e7284
     - path: miniwdl_run/call-consensus_qc/work/NUM_N
-      md5sum: 8ad46215ff3252d17d9e062e6f84d472
+      md5sum: fd7c21d6426a67e58606f4f5af3bcb0c
     - path: miniwdl_run/call-consensus_qc/work/NUM_TOTAL
       md5sum: 64887188f1a0c0176ed5ad2e108d1046
     - path: miniwdl_run/call-consensus_qc/work/PERCENT_REF_COVERAGE
-      md5sum: 7f9226df824c26eaa79412a2ba1390ab
+      md5sum: 3f5b244cd6683efff0dec4915a795267
     - path: miniwdl_run/call-consensus_qc/work/_miniwdl_inputs/0/clearlabs.consensus.fasta
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-fastq_scan_clean_reads/command
@@ -206,7 +206,7 @@
     - path: miniwdl_run/call-nextclade_v3/work/clearlabs.consensus.nextclade.json
     - path: miniwdl_run/call-nextclade_v3/work/clearlabs.consensus.nextclade.tsv
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.aligned.fasta
-      md5sum: 1ba0d3575483bc24b6cf4565f0ef797f
+      md5sum: fd2c9f76bda2f2df78cdbae2e82d7430
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.csv
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.ndjson
     - path: miniwdl_run/call-nextclade_v3/work/nextclade_dataset_dir/genome_annotation.gff3
@@ -224,7 +224,7 @@
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.N.fasta
       md5sum: 22756e66f3b0fe8a00d685fc145edaf5
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.ORF1a.fasta
-      md5sum: 8d49bc37ee2d3506cd7bf67cc98d9070
+      md5sum: 397e034fe525d393a8b5b500df0c75c0
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.ORF1b.fasta
       md5sum: 9827745ec4fe4976ad6c063b0f097cb3
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.ORF3a.fasta
@@ -324,7 +324,7 @@
     - path: miniwdl_run/call-stats_n_coverage/work/clearlabs.flagstat.txt
       md5sum: f5d6f96c87d96ebe60358948d310f223
     - path: miniwdl_run/call-stats_n_coverage/work/clearlabs.stats.txt
-      md5sum: 2ec4deb812d1cb840d67666114726070
+      md5sum: 091d3db26cbfd2c804dd7348f4b09087
     - path: miniwdl_run/call-stats_n_coverage_primtrim/command
       md5sum: 2974f886e1959cd5eaae5e495c91f7cc
     - path: miniwdl_run/call-stats_n_coverage_primtrim/inputs.json
@@ -355,9 +355,9 @@
     - path: miniwdl_run/call-stats_n_coverage_primtrim/work/clearlabs.flagstat.txt
       md5sum: f5d6f96c87d96ebe60358948d310f223
     - path: miniwdl_run/call-stats_n_coverage_primtrim/work/clearlabs.stats.txt
-      md5sum: c91dddf8c6282849df368c0a27535da0
+      md5sum: 60a3f910312be4cf39bcd3116b2a161a
     - path: miniwdl_run/call-vadr/command
-      md5sum: 7423ff35f0c469bb4390496eafc2320e
+      md5sum: f7dbfd3d59316546682133d7aae17fad
     - path: miniwdl_run/call-vadr/inputs.json
       contains: ["assembly_length_unambiguous", "genome_fasta", "fasta"]
     - path: miniwdl_run/call-vadr/outputs.json
@@ -375,11 +375,11 @@
       md5sum: 2562e7c1fd77507231c7059bb7f09a93
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus.vadr.tar.gz
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.NC_045512.CDS.1.fa
-      md5sum: 01f8699ad0440b85c6f3459cc8807bed
+      md5sum: d7167d1728389a9a48fbdbdb1f0f1675
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.NC_045512.CDS.2.fa
-      md5sum: 78b1d8284142225dd6431754153a73b7
+      md5sum: 37ae1c39a53eef5d26944228b531a478
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.NC_045512.gene.1.fa
-      md5sum: 9acee3886131673087ff77f0a6dc488a
+      md5sum: 5fe92e7fb7cf3fa33f74974e04faef48
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.NC_045512.gene.2.fa
       md5sum: 293fb93b99a93927ffac6411a057799d
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.NC_045512.mat_peptide.1.fa
@@ -400,15 +400,15 @@
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.dcr
       md5sum: d9b5295b718f16cf523fa42c69c67f7f
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.fail.fa
-      md5sum: 5b11a0cec698d10a5c44ff0048ee63b4
+      md5sum: 2ad8aee5a998d9f4cef4bbe9a60f6f44
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.fail.list
       md5sum: 7b7182529739b37ce90f7eb74301fe1f
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.fail.tbl
       md5sum: ceee7788ffea5737bfc99a51905cc8fc
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.filelist
       md5sum: 8736d943b1e4b18906cf0cad4be881f9
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.ftr
-      md5sum: b2f5f7bdeec14292a089bb0d968c6f3b
+      md5sum: d4809c38b77c7ba477ef58090fb32f86
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.log
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.mdl
       md5sum: 43735aaecb85b313c6b6c9789b324337
@@ -419,7 +419,7 @@
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.pass.tbl
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.rpn
-      md5sum: 5e323f8edc70f5fd4d2636ed650c96ea
+      md5sum: ba4815d0793abb64566d6d303f20831d
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.sda
       md5sum: 7a6d49ee8d1354238dfefeeab63ae25f
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.seqstat
@@ -429,16 +429,16 @@
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.sqa
       md5sum: 1efac9aeee74d0cdfc7467799905fd6d
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus/clearlabs.consensus.vadr.sqc.txt
-      md5sum: 77e5d6c111753ac47a6168f48b04be18
+      md5sum: 633508465581359ba1aba2f43ea1faf9
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus_trimmed.fasta
-      md5sum: 5b11a0cec698d10a5c44ff0048ee63b4
+      md5sum: 2ad8aee5a998d9f4cef4bbe9a60f6f44
     - path: miniwdl_run/call-vadr/work/clearlabs.consensus_vadr-fasta-files.zip
     - path: miniwdl_run/call-vadr/work/vadr_fasta_files/clearlabs.consensus.vadr.NC_045512.CDS.1.fa
-      md5sum: 01f8699ad0440b85c6f3459cc8807bed
+      md5sum: d7167d1728389a9a48fbdbdb1f0f1675
     - path: miniwdl_run/call-vadr/work/vadr_fasta_files/clearlabs.consensus.vadr.NC_045512.CDS.2.fa
-      md5sum: 78b1d8284142225dd6431754153a73b7
+      md5sum: 37ae1c39a53eef5d26944228b531a478
     - path: miniwdl_run/call-vadr/work/vadr_fasta_files/clearlabs.consensus.vadr.NC_045512.gene.1.fa
-      md5sum: 9acee3886131673087ff77f0a6dc488a
+      md5sum: 5fe92e7fb7cf3fa33f74974e04faef48
     - path: miniwdl_run/call-vadr/work/vadr_fasta_files/clearlabs.consensus.vadr.NC_045512.gene.2.fa
       md5sum: 293fb93b99a93927ffac6411a057799d
     - path: miniwdl_run/call-vadr/work/vadr_fasta_files/clearlabs.consensus.vadr.NC_045512.mat_peptide.1.fa
@@ -450,7 +450,7 @@
     - path: miniwdl_run/call-vadr/work/vadr_fasta_files/clearlabs.consensus.vadr.NC_045512.stem_loop.2.fa
       md5sum: 4acfd69ec183f3a9374fbb4c3cce491f
     - path: miniwdl_run/call-vadr/work/vadr_fasta_files/clearlabs.consensus.vadr.fail.fa
-      md5sum: 5b11a0cec698d10a5c44ff0048ee63b4
+      md5sum: 2ad8aee5a998d9f4cef4bbe9a60f6f44
     - path: miniwdl_run/call-vadr/work/vadr_fasta_files/clearlabs.consensus.vadr.pass.fa
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-version_capture/inputs.json

diff --git a/tests/workflows/theiacov/test_wf_theiacov_ont.yml b/tests/workflows/theiacov/test_wf_theiacov_ont.yml
@@ -45,27 +45,19 @@
     - path: miniwdl_run/call-consensus/work/REFERENCE_GENOME
       md5sum: 0e6efd549c8773f9a2f7a3e82619ee61
     - path: miniwdl_run/call-consensus/work/VERSION
-      md5sum: f3528ff85409c70100063c55ad75612b
+      md5sum: b50a846b8b57f344bcedad5c6962b2c7
     - path: miniwdl_run/call-consensus/work/_miniwdl_inputs/0/artic-v3.primers.bed
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-consensus/work/_miniwdl_inputs/0/artic_ncov2019_ont.fastq
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: miniwdl_run/call-consensus/work/ont.1.hdf
     - path: miniwdl_run/call-consensus/work/ont.1.vcf
-    - path: miniwdl_run/call-consensus/work/ont.2.hdf
     - path: miniwdl_run/call-consensus/work/ont.2.vcf
-    - path: miniwdl_run/call-consensus/work/ont.alignreport.er
-    - path: miniwdl_run/call-consensus/work/ont.alignreport.txt
     - path: miniwdl_run/call-consensus/work/ont.consensus.fasta
-      md5sum: cdde2d8b7efeb498806c5c2cfc522675
+      md5sum: 3950a30ee2fe99e53f2565723480867a
     - path: miniwdl_run/call-consensus/work/ont.coverage_mask.txt
       md5sum: afe03fabc8dd227e790deddd6402e9a5
     - path: miniwdl_run/call-consensus/work/ont.fail.vcf
     - path: miniwdl_run/call-consensus/work/ont.fastq.gz
-    - path: miniwdl_run/call-consensus/work/ont.medaka.consensus.fasta
-      md5sum: d36b7c665aa4127f0a6e8dbc562eea3e
-    - path: miniwdl_run/call-consensus/work/ont.merged.gvcf.vcf.gz
-    - path: miniwdl_run/call-consensus/work/ont.merged.gvcf.vcf.gz.tbi
     - path: miniwdl_run/call-consensus/work/ont.merged.vcf.gz
     - path: miniwdl_run/call-consensus/work/ont.merged.vcf.gz.tbi
     - path: miniwdl_run/call-consensus/work/ont.minion.log.txt
@@ -77,25 +69,17 @@
       md5sum: 4ca7d9fd06b9cdf379c2cf02b9fd6d0e
     - path: miniwdl_run/call-consensus/work/ont.primers.vcf
     - path: miniwdl_run/call-consensus/work/ont.primersitereport.txt
-      md5sum: cffee67632a262eeb947cea9cee0b4c1
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-consensus/work/ont.primertrimmed.rg.sorted.bam
     - path: miniwdl_run/call-consensus/work/ont.primertrimmed.rg.sorted.bam.bai
     - path: miniwdl_run/call-consensus/work/ont.sorted.bam
     - path: miniwdl_run/call-consensus/work/ont.sorted.bam.bai
     - path: miniwdl_run/call-consensus/work/ont.trimmed.rg.sorted.bam
     - path: miniwdl_run/call-consensus/work/ont.trimmed.rg.sorted.bam.bai
-    - path: miniwdl_run/call-consensus/work/ont.vcfcheck.log
-    - path: miniwdl_run/call-consensus/work/ont.vcfreport.txt
-      md5sum: 69131186223267b3ae6621cb8ef4eecd
-    - path: miniwdl_run/call-consensus/work/primer-schemes/SARS-CoV-2/Vuser/SARS-CoV-2.reference.fasta
-      md5sum: b9b67235a2d9d0b0d7f531166ffefd41
-    - path: miniwdl_run/call-consensus/work/primer-schemes/SARS-CoV-2/Vuser/SARS-CoV-2.reference.fasta.fai
-    - path: miniwdl_run/call-consensus/work/primer-schemes/SARS-CoV-2/Vuser/SARS-CoV-2.scheme.bed
-      md5sum: d5ad850f8c610dc45162957ab84530d6
     - path: miniwdl_run/call-consensus_qc/command
-      md5sum: 3f21640edd4e1691fec5f5e2cc061d97
+      md5sum: 31dfee1552f68e5c6f72431458a33535
     - path: miniwdl_run/call-consensus_qc/inputs.json
-      contains: ["assembly_fasta", "medaka"]
+      contains: ["assembly_fasta"]
     - path: miniwdl_run/call-consensus_qc/outputs.json
       contains: ["consensus_qc", "number_N", "percent_reference_coverage"]
     - path: miniwdl_run/call-consensus_qc/stderr.txt
@@ -114,7 +98,7 @@
       md5sum: cd5d3fde6b7f2417ec8ed3e7d5e85b28
     - path: miniwdl_run/call-consensus_qc/work/PERCENT_REF_COVERAGE
       md5sum: 1684062540bab8897921ed5e40c747cf
-    - path: miniwdl_run/call-consensus_qc/work/_miniwdl_inputs/0/ont.medaka.consensus.fasta
+    - path: miniwdl_run/call-consensus_qc/work/_miniwdl_inputs/0/ont.consensus.fasta
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-nextclade_v3/command
     - path: miniwdl_run/call-nextclade_v3/inputs.json
@@ -128,10 +112,9 @@
       contains: ["wdl", "theiacov_ont", "done"]
     - path: miniwdl_run/call-nextclade_v3/work/NEXTCLADE_VERSION
       md5sum: 70aa6879bf9f0e8ba2b9953b0d4a2216
-    - path: miniwdl_run/call-nextclade_v3/work/_miniwdl_inputs/0/ont.medaka.consensus.fasta
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: miniwdl_run/call-nextclade_v3/work/_miniwdl_inputs/0/ont.consensus.fasta
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.aligned.fasta
-      md5sum: 9af2828c3169f789cd1266960c8595da
+      md5sum: e89d162b1de311166f574fdd72bb889b
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.csv
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.ndjson
     - path: miniwdl_run/call-nextclade_v3/work/nextclade_dataset_dir/genome_annotation.gff3
@@ -141,32 +124,32 @@
     - path: miniwdl_run/call-nextclade_v3/work/nextclade_dataset_dir/tree.json
     - path: miniwdl_run/call-nextclade_v3/work/nextclade_dataset_dir/pathogen.json
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.E.fasta
-      md5sum: b84502318ddddc339eae05c5eb2a1ff8
+      md5sum: ed16c9347bfc40c036bfd6696357f276
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.M.fasta
-      md5sum: 7b4b60c7ed0c3b02be1095913c8a19e0
+      md5sum: 665563797b25a2f8c317f1de5bfd3100
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.N.fasta
-      md5sum: b07a3ee9b75d9a5e85561e2fed5cccfc
+      md5sum: 37f9705280adf60301e46846e4244df2
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.ORF1a.fasta
-      md5sum: 28e0341110fd8c446ea1c4a2c14bcff1
+      md5sum: abafdd46ce000786c30719975cbae293
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.ORF1b.fasta
-      md5sum: 5fea3fa7473ea78ce7d67840377fe5e8
+      md5sum: 2f92eb27dd46628b9fc92e72a22995e3
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.ORF3a.fasta
-      md5sum: 9a53be681f7d92d46200438d03f8a16b
+      md5sum: f0a567079160c44c65e6702373223ce1
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.ORF6.fasta
-      md5sum: c1d610f9e45acd3915e40f0d643f0188
+      md5sum: 01f0c1f6fc3f5ab763d687548926b7e5
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.ORF7a.fasta
-      md5sum: a209e21c4a9a49649746b39ee449331f
+      md5sum: 0940fd46f48d302bc5d369aca02da8fb
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.ORF7b.fasta
-      md5sum: 4ba532a9baaf5454f662eb67fa2caa74
+      md5sum: 7c1e739e9036385620101b55689f1a23
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.ORF8.fasta
-      md5sum: c9b62e72831fa3198ebd28758aca5b29
+      md5sum: b6fea260f3a7ab5fcc9c8745f4ae038b
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.ORF9b.fasta
-      md5sum: 0f55e05f70734e109cca95918da37881
+      md5sum: 44afb04dc2cfa4a89c3cf5c83093cfe5
     - path: miniwdl_run/call-nextclade_v3/work/nextclade.cds_translation.S.fasta
-      md5sum: 9efd0dad1c8fc8bd802f20a6d5105bb0
-    - path: miniwdl_run/call-nextclade_v3/work/ont.medaka.consensus.nextclade.auspice.json
-    - path: miniwdl_run/call-nextclade_v3/work/ont.medaka.consensus.nextclade.json
-    - path: miniwdl_run/call-nextclade_v3/work/ont.medaka.consensus.nextclade.tsv
+      md5sum: b3680ba0128f39230d9cbaf62edf1f23
+    - path: miniwdl_run/call-nextclade_v3/work/ont.consensus.nextclade.auspice.json
+    - path: miniwdl_run/call-nextclade_v3/work/ont.consensus.nextclade.json
+    - path: miniwdl_run/call-nextclade_v3/work/ont.consensus.nextclade.tsv
     - path: miniwdl_run/call-nextclade_output_parser/command
       md5sum: 6b2d20d9df7c656a76755a4048acf3ec
     - path: miniwdl_run/call-nextclade_output_parser/inputs.json
@@ -188,7 +171,7 @@
       md5sum: dc20c75a91e9d9de3d98af59d035f17c
     - path: miniwdl_run/call-nextclade_output_parser/work/TAMIFLU_AASUBS
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: miniwdl_run/call-nextclade_output_parser/work/_miniwdl_inputs/0/ont.medaka.consensus.nextclade.tsv
+    - path: miniwdl_run/call-nextclade_output_parser/work/_miniwdl_inputs/0/ont.consensus.nextclade.tsv
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-nextclade_output_parser/work/input.tsv
     - path: miniwdl_run/call-pangolin4/command
@@ -215,8 +198,7 @@
       md5sum: 36f64a1cd7c6844309e8ad2121358088
     - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL
       md5sum: dfd90750c8776f46bad1de214c1d1a57
-    - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/ont.medaka.consensus.fasta
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/ont.consensus.fasta
     - path: miniwdl_run/call-pangolin4/work/ont.pangolin_report.csv
     - path: miniwdl_run/call-raw_check_reads/command
       md5sum: 5df9a70c852960f82c84c7da611cd177
@@ -293,11 +275,9 @@
       contains: ["wdl", "theiacov_ont", "done"]
     - path: miniwdl_run/call-vadr/work/NUM_ALERTS
       md5sum: 897316929176464ebc9ad085f31e7284
-    - path: miniwdl_run/call-vadr/work/_miniwdl_inputs/0/ont.medaka.consensus.fasta
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: miniwdl_run/call-vadr/work/ont.medaka.consensus.vadr.alerts.tsv
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: miniwdl_run/call-vadr/work/ont.medaka.consensus.vadr.tar.gz
+    - path: miniwdl_run/call-vadr/work/_miniwdl_inputs/0/ont.consensus.fasta
+    - path: miniwdl_run/call-vadr/work/ont.consensus.vadr.alerts.tsv
+    - path: miniwdl_run/call-vadr/work/ont.consensus.vadr.tar.gz
     - path: miniwdl_run/call-version_capture/inputs.json
     - path: miniwdl_run/call-version_capture/outputs.json
       contains: ["version_capture", "date", "version"]