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Dev #143

Merged
merged 61 commits into from
Nov 27, 2024
Merged

Dev #143

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2b88eb4
allowed un-compressed input formats
mattheww95 Oct 22, 2024
41143bd
updated changelog
mattheww95 Oct 22, 2024
2692d27
updated workflow for linting
mattheww95 Oct 22, 2024
9d25154
began updating to use nf-core 3.0.1
mattheww95 Oct 22, 2024
98d572f
updated config to pass linting
mattheww95 Oct 22, 2024
4f1a60f
added missing test files
mattheww95 Oct 22, 2024
0299ae2
Merge pull request #137 from phac-nml/issue-60
mattheww95 Oct 23, 2024
365f47b
added sample irida_next sample field option
mattheww95 Oct 24, 2024
91affcd
updated test datasets
mattheww95 Oct 24, 2024
7edf2aa
identified sticking point for sample names not being passed to the ir…
mattheww95 Oct 24, 2024
351a8f1
updated iridanext external name id
mattheww95 Oct 28, 2024
acdb884
updated changelog and docs
mattheww95 Oct 28, 2024
631b094
updated test samplesheets
mattheww95 Oct 28, 2024
dcdce6d
udpated samples sheet names
mattheww95 Oct 28, 2024
fd4ea24
updated inx id parsing
mattheww95 Oct 28, 2024
0d81ebf
updated sample sheet parsing
mattheww95 Oct 28, 2024
318df6a
sample sheet for inx now matches new format
mattheww95 Oct 29, 2024
a4de4a3
updated sample sheet for test profile
mattheww95 Oct 29, 2024
c036fb5
updated tests
mattheww95 Oct 29, 2024
6cb6d8c
updating commits for feedback
mattheww95 Oct 31, 2024
2f0c3cc
updated sample sheet name
mattheww95 Oct 31, 2024
db34308
updated samplesheets
mattheww95 Oct 31, 2024
c410a3f
reverted samplesheet names
mattheww95 Oct 31, 2024
d13761c
changed samplesheet headers
mattheww95 Oct 31, 2024
0c6e6d1
updated sample sheet name
mattheww95 Oct 31, 2024
419500b
updated test samplesheet
mattheww95 Oct 31, 2024
d1e5609
updated external_id parsing, tests will fail as path locations need t…
mattheww95 Oct 31, 2024
a48fb95
updated output of flattened sample reports
mattheww95 Nov 1, 2024
39c8505
fixed erroneous comment
mattheww95 Nov 1, 2024
14653fb
updated sample field orders
mattheww95 Nov 5, 2024
9c0bad4
updated logic for renaming sample id
mattheww95 Nov 5, 2024
c8827fe
updated sample parsing
mattheww95 Nov 6, 2024
db5f420
updated docs, changelog and nextflow_schema.json
mattheww95 Nov 6, 2024
9ed27b8
Update samplesheet-small-assembly-inx.csv
mattheww95 Nov 6, 2024
52af4a9
updated test cases
mattheww95 Nov 6, 2024
eb75969
updating inputcheck tests
mattheww95 Nov 6, 2024
45ce5a2
added missing files
mattheww95 Nov 6, 2024
eec62b3
updated tests
mattheww95 Nov 6, 2024
733db44
fixed failing tests
mattheww95 Nov 7, 2024
71260a9
updated tests
mattheww95 Nov 7, 2024
3c4e1c4
fixed my own mistakes
mattheww95 Nov 7, 2024
738943b
fixed failing test
mattheww95 Nov 7, 2024
b1e60dd
swapped external_id and id
mattheww95 Nov 8, 2024
70d0291
updating information before the weekend
mattheww95 Nov 8, 2024
6ba57b0
fixed stupid name issue report keys not found
mattheww95 Nov 12, 2024
a2c56a8
fixed failig test case
mattheww95 Nov 12, 2024
a1c3f3e
updated changelog
mattheww95 Nov 12, 2024
899e35b
updated changelog
mattheww95 Nov 12, 2024
a084717
Sample ID is now used as the column names in outputs
mattheww95 Nov 21, 2024
ce1b8e6
fixed label indexing
mattheww95 Nov 21, 2024
822695d
updated sample sheet usage and restricted the usage of periods in names
mattheww95 Nov 21, 2024
c4df975
updated input check tests
mattheww95 Nov 22, 2024
839bc81
Clarified valid characters in error message.
apetkau Nov 26, 2024
ae296a3
Forgot I could not have quotes in error string
apetkau Nov 26, 2024
f853ce8
Merge pull request #140 from phac-nml/inx_id
apetkau Nov 26, 2024
5c9e50c
updated listeria parameter
mattheww95 Nov 27, 2024
07a1231
updated changelog
mattheww95 Nov 27, 2024
58471c9
updated wordslist
mattheww95 Nov 27, 2024
42236fd
updated changelog
mattheww95 Nov 27, 2024
6e6758b
updated tests for listeria
mattheww95 Nov 27, 2024
9170fbc
Merge pull request #142 from phac-nml/listeriam
mattheww95 Nov 27, 2024
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sample sheet for inx now matches new format
mattheww95 committed Oct 29, 2024
commit 318df6a330e44689aa564b745badc25bf2b831ec
2 changes: 1 addition & 1 deletion tests/data/samplesheets/samplesheet-small-assembly-inx.csv
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
sample_name,sample,fastq_1,fastq_2,long_reads,assembly
sample,sample_name,fastq_1,fastq_2,long_reads,assembly
INX,short,https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/reads/1_R1.fq,https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/reads/1_R2.fq,,