diff --git a/README.md b/README.md index 5e3b0471cd7df606e4685abcf800148120395e68..3125a563e4f3ee01a13484a082acc0a3005f0794 100644 --- a/README.md +++ b/README.md @@ -218,63 +218,6 @@ your run. bash run.sh ``` -#### Additional information - -The metadata field names in the LabKey instance and those in the parameters -in the Snakemake workflow have different names. A mapping between LabKey -field identifiers and Snakemake parameters is listed below: - -Labkey | Snakemake ---- | --- -Entry date | entry_date -Path to FASTQ file(s) | fastq_path -Condition name | condition -Replicate name | replicate_name -End type (PAIRED or SINGLE) | seqmode -Name of Mate1 FASTQ file | fq1 -Name of Mate2 FASTQ file | fq2 -Direction of Mate1 (SENSE, ANTISENSE or RANDOM) | mate1_direction -Direction of Mate2 (SENSE, ANTISENSE or RANDOM) | mate2_direction -5' adapter of Mate1 | fq1_5p -3' adapter of Mate1 | fq1_3p -5' adapter of Mate2 | fq2_5p -3' adapter of Mate2 | fq2_3p -Fragment length mean | mean -Fragment length SD | sd -Quality control flag (PASSED or FAILED) | quality_control_flag -Checksum of raw Mate1 FASTQ file | mate1_checksum -Checksum of raw Mate2 FASTQ file | mate2_checksum -Name of metadata file | metadata -Name of quality control file for Mate1 | mate1_quality -Name of quality control file for Mate2 | mate2_quality -Organism | organism -Taxon ID | taxon_id -Name of Strain / Isolate / Breed / Ecotype | strain_name -Strain / Isolate / Breed / Ecotype ID | strain_id -Biomaterial provider | biomaterial_provider -Source / tissue name | source_name -Tissue code | tissue_code -Additional tissue description | tissue_description -Genotype short name | genotype_name -Genotype description | genotype_description -Disease short name | disease_name -Disease description | disease_description -Abbreviation for treatment | treatment -Treatment description | treatment_description -Gender | gender -Age | age -Developmental stage | development_stage -Passage number | passage_number -Sample preparation date (YYYY-MM-DD) | sample_prep_date -Prepared by | prepared_by -Documentation | documentation -Name of protocol file | protocol_file -Sequencing date (YYYY-MM-DD) | seq_date -Sequencing instrument | seq_instrument -Library preparation kit | library_kit -Cycles | cycles -Molecule | molecule -Contaminant sequences | contaminant_seqs [conda]: <https://docs.conda.io/projects/conda/en/latest/index.html> [profiles]: <https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles>