taxprofiler :add broken input samplesheet

README.md

@@ -197,7 +197,7 @@ rm *dmp *txt *gz *prt *zip
 
 KrakenUniq version 1.0.0
 
-> ⚠️  This database _does not_ use the specified files used in the other databases, as this built into a database that was tool large.
+> ⚠️ This database _does not_ use the specified files used in the other databases, as this built into a database that was tool large.
 
 This database includes the SARS-CoV2 genome used on the nf-core/modules test-datasets repository (NCBI Accession: MT192765.1).
 
@@ -221,13 +221,12 @@ mkdir gtdb-genomes
 ## Copy the downloaded fasta files for Penicillium roqueforti and Human genome mitochondral to folder gtdb-genomes.
 
 ## Rename the file for Penicillium roqueforti to match the seqid2taxid.map file
-mv GCF_015533775.1_ASM1553377v1_genomic.fna.gz NW_024067565.1.fna.gz 
+mv GCF_015533775.1_ASM1553377v1_genomic.fna.gz NW_024067565.1.fna.gz
 
 kmcp compute -k 21 -n 10 -l 150 -O tmp-k21-n10-l150 -I gtdb-genomes
-kmcp index -f 0.3 -n 1 -j 32 -I tmp-k21-n10-l150 -O gtdb.kmcp 
+kmcp index -f 0.3 -n 1 -j 32 -I tmp-k21-n10-l150 -O gtdb.kmcp
 ```
 
-
 ## Taxprofiler AWS Full Test specific-information
 
 ### FASTQ
@@ -237,13 +236,13 @@ The main AWS full test data used for nf-core/taxprofiler is from [Meslier et al.
 They were selected as a benchmarking dataset containing a semi-complex microbial community with strains that have known reference genomes, and with multiple sequencing runs one of sample of the Illumina dataset. ENA Experiment IDs are as follows
 
 - ONT MiniION R9
-    - ERX9314125
-    - ERX9314126
-    - ERR9765782
+  - ERX9314125
+  - ERX9314126
+  - ERR9765782
 - Illumina HiSeq 3000
-    - ERX9314116
-    - ERX9314117
-    - ERX9314118 (x2 runs)
+  - ERX9314116
+  - ERX9314117
+  - ERX9314118 (x2 runs)
 
 FASTQ files for the `samplesheet_full.tsv` are stored on the [EBI ENA servers](https://www.ebi.ac.uk/ena/browser/view/PRJEB52977)
 
@@ -536,7 +535,6 @@ awk 'FNR==NR {f2[$1]=$2;next} /^>/ { for (i in f2) { if (index(substr($1,2), i))
 
 We can copy the previously downloaded NCBI taxonomy files into the Kaiju working directory
 
-
 ```bash
 cp nodes.dmp names.dmp meslier2022/kaiju/
 ```
@@ -689,6 +687,23 @@ KAIJU
 rm meslier2022/kaiju/*.{bwt,sa}
 ```
 
+## Broken Samplesheets
+
+We also hold 'broken' samplesheets for testing input schema validation.
+
+- `broken_samplesheets/test_database_duplicate_tool_db_name.csv`: duplicated rows to test the unique entires of `tool` and `db_name`
+- `broken_samplesheets/test_samplesheet_duplicate_fasta.csv`: duplicated FASTA file to test the unique entry of `fasta`
+- `broken_samplesheets/test_samplesheet_duplicate_fastq.csv`: duplicated FASTQ file to test the unique entries of `fastq_1` or `fastq_2`
+- `broken_samplesheets/test_samplesheet_duplicate_sample_run_accession.csv`: duplicated row to test the unique entries of `sample` and `run_accession`
+- `broken_samplesheets/test_samplesheet_sample_with_space.csv`: add a space to the `sample` entry
+- `broken_samplesheets/test_database_missing_tool.csv`: missing `tool` entry in the database
+- `broken_samplesheets/test_database_missing_db_name.csv`: missing `db_name` entry in the database
+- `broken_samplesheets/test_database_missing_db_path.csv`: missing `db_path` entry in the database
+- `broken_samplesheets/test_database_missing_db_type.csv`: missing `db_type` entry to test empty values in the database
+- `broken_samplesheets/test_samplesheet_missing_sample.csv`: missing `sample` entry in the samplesheet
+- `broken_samplesheets/test_samplesheet_missing_run_accession.csv`: missing `run_accession.csv` entry in the samplesheet
+- `broken_samplesheets/test_samplesheet_missing_instrument_platform.csv`: missing `instrument_platform` column in the samplesheet
+
 ## Support
 
 For further information or help, don't hesitate to get in touch on our [Slack organisation](https://nf-co.re/join/slack) (a tool for instant messaging).

broken_samplesheets/test_database_duplicate_tool_db_name.csv

@@ -0,0 +1,18 @@
+tool,db_name,db_params,db_type,db_path
+malt,malt85,-id 85,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/malt/testdb-malt.tar.gz
+malt,malt95,-id 90,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/malt/testdb-malt.tar.gz
+bracken,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/bracken/testdb-bracken.tar.gz
+kraken2,db2,--quick,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kraken2/testdb-kraken2.tar.gz
+kraken2,db2,--quick,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kraken2/testdb-kraken2.tar.gz
+centrifuge,db3,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/centrifuge/test-db-centrifuge.tar.gz
+centrifuge,db3,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/centrifuge/test-db-centrifuge.tar.gz
+kaiju,db5,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+kaiju,db6,-m 50,long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+kaiju,db7,,short;long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+diamond,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+diamond,db2,--long-reads,long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+diamond,db3,,short;long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+ganon,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/ganon/test-db-ganon.tar.gz
+metaphlan,metaphlan3,--mpa3,short,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz
+metaphlan,metaphlan4,,short,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan4_database.tar.gz
+kmcp,db1,;-m 0,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kmcp/test-db-kmcp.tar.gz

broken_samplesheets/test_database_missing_db_name.csv

@@ -0,0 +1,16 @@
+tool,db_name,db_params,db_type,db_path
+malt,malt85,-id 85,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/malt/testdb-malt.tar.gz
+malt,malt95,-id 90,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/malt/testdb-malt.tar.gz
+bracken,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/bracken/testdb-bracken.tar.gz
+kraken2,,--quick,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kraken2/testdb-kraken2.tar.gz
+centrifuge,db3,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/centrifuge/test-db-centrifuge.tar.gz
+kaiju,db5,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+kaiju,db6,-m 50,long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+kaiju,db7,,short;long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+diamond,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+diamond,db2,--long-reads,long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+diamond,db3,,short;long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+ganon,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/ganon/test-db-ganon.tar.gz
+metaphlan,metaphlan3,--mpa3,short,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz
+metaphlan,metaphlan4,,short,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan4_database.tar.gz
+kmcp,db1,;-m 0,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kmcp/test-db-kmcp.tar.gz

broken_samplesheets/test_database_missing_db_path.csv

@@ -0,0 +1,16 @@
+tool,db_name,db_params,db_type,db_path
+malt,malt85,-id 85,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/malt/testdb-malt.tar.gz
+malt,malt95,-id 90,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/malt/testdb-malt.tar.gz
+bracken,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/bracken/testdb-bracken.tar.gz
+kraken2,db2,--quick,short,,
+centrifuge,db3,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/centrifuge/test-db-centrifuge.tar.gz
+kaiju,db5,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+kaiju,db6,-m 50,long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+kaiju,db7,,short;long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+diamond,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+diamond,db2,--long-reads,long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+diamond,db3,,short;long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+ganon,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/ganon/test-db-ganon.tar.gz
+metaphlan,metaphlan3,--mpa3,short,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz
+metaphlan,metaphlan4,,short,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan4_database.tar.gz
+kmcp,db1,;-m 0,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kmcp/test-db-kmcp.tar.gz

broken_samplesheets/test_database_missing_db_type.csv

@@ -0,0 +1,16 @@
+tool,db_name,db_params,db_type,db_path
+malt,malt85,-id 85,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/malt/testdb-malt.tar.gz
+malt,malt95,-id 90,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/malt/testdb-malt.tar.gz
+bracken,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/bracken/testdb-bracken.tar.gz
+kraken2,db2,--quick,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kraken2/testdb-kraken2.tar.gz
+centrifuge,db3,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/centrifuge/test-db-centrifuge.tar.gz
+kaiju,db5,,,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+kaiju,db6,-m 50,long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+kaiju,db7,,short;long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+diamond,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+diamond,db2,--long-reads,long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+diamond,db3,,short;long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+ganon,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/ganon/test-db-ganon.tar.gz
+metaphlan,metaphlan3,--mpa3,short,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz
+metaphlan,metaphlan4,,short,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan4_database.tar.gz
+kmcp,db1,;-m 0,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kmcp/test-db-kmcp.tar.gz

broken_samplesheets/test_database_missing_tool.csv

@@ -0,0 +1,16 @@
+tool,db_name,db_params,db_type,db_path
+,malt85,-id 85,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/malt/testdb-malt.tar.gz
+malt,malt95,-id 90,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/malt/testdb-malt.tar.gz
+bracken,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/bracken/testdb-bracken.tar.gz
+kraken2,db2,--quick,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kraken2/testdb-kraken2.tar.gz
+centrifuge,db3,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/centrifuge/test-db-centrifuge.tar.gz
+kaiju,db5,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+kaiju,db6,-m 50,long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+kaiju,db7,,short;long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/kaiju.tar.gz
+diamond,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+diamond,db2,--long-reads,long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+diamond,db3,,short;long,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/diamond/testdb-diamond.dmnd
+ganon,db1,,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/ganon/test-db-ganon.tar.gz
+metaphlan,metaphlan3,--mpa3,short,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz
+metaphlan,metaphlan4,,short,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan4_database.tar.gz
+kmcp,db1,;-m 0,short,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kmcp/test-db-kmcp.tar.gz

broken_samplesheets/test_samplesheet_duplicate_fasta.csv

@@ -0,0 +1,9 @@
+sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
+2611,ERR5766174,ILLUMINA,,,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fasta/ERX5474930_ERR5766174_1.fa.gz
+2611_dup,ERR5766174_dup,ILLUMINA,,,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fasta/ERX5474930_ERR5766174_1.fa.gz
+2612,ERR5766176,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_2.fastq.gz,
+2612,ERR5766176_B,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_B_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_B_2.fastq.gz,
+2612,ERR5766180,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474936_ERR5766180_1.fastq.gz,,
+2613,ERR5766181,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_2.fastq.gz,
+ERR3201952,ERR3201952,OXFORD_NANOPORE,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERR3201952.fastq.gz,,
+2614,ERR3201952,OXFORD_NANOPORE,,,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fasta/ERR3201952_dup.fa.gz

broken_samplesheets/test_samplesheet_duplicate_fastq.csv

@@ -0,0 +1,8 @@
+sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
+2611,ERR5766174,ILLUMINA,,,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fasta/ERX5474930_ERR5766174_1.fa.gz
+2612,ERR5766176,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_2.fastq.gz,
+2612,ERR5766176_B,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_2.fastq.gz,
+2612,ERR5766180,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474936_ERR5766180_1.fastq.gz,,
+2613,ERR5766181,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_2.fastq.gz,
+ERR3201952,ERR3201952,OXFORD_NANOPORE,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERR3201952.fastq.gz,,
+2614,ERR3201952,OXFORD_NANOPORE,,,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fasta/ERR3201952_dup.fa.gz

broken_samplesheets/test_samplesheet_duplicate_sample_run_accession.csv

@@ -0,0 +1,8 @@
+sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
+2611,ERR5766174,ILLUMINA,,,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fasta/ERX5474930_ERR5766174_1.fa.gz
+2612,ERR5766176,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_2.fastq.gz,
+2612,ERR5766176,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_B_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_B_2.fastq.gz,
+2612,ERR5766180,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474936_ERR5766180_1.fastq.gz,,
+2613,ERR5766181,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_2.fastq.gz,
+ERR3201952,ERR3201952,OXFORD_NANOPORE,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERR3201952.fastq.gz,,
+2614,ERR3201952,OXFORD_NANOPORE,,,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fasta/ERR3201952_dup.fa.gz

broken_samplesheets/test_samplesheet_missing_instrument_platform.csv

@@ -0,0 +1,8 @@
+sample,run_accession,fastq_1,fastq_2,fasta
+2611,ERR5766174,,,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fasta/ERX5474930_ERR5766174_1.fa.gz
+2612,ERR5766176,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_2.fastq.gz,
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