dont know how that got removed

config.yml

@@ -0,0 +1,38 @@
+all:
+    project_dir: "/home/danielsg/16S_QIIME2/test"
+    mux_dir: "multiplexed_fastq"
+    mapping: "test_mapping_file.tsv"
+    admin_email: "[email protected]"
+
+#try revcomp if you are getting 0 reads when demultiplexing
+demux:
+    mismatch: 0
+    revcomp: false
+
+denoise:
+    trim_left_f: 0
+    trunc_len_f: 240
+    trim_left_r: 0
+    trunc_len_r: 240
+    n_threads: 6
+
+taxonomy:
+    classifier_fp: "/home/danielsg/16S_QIIME2/QIIME2_data/gg-13-8-99-nb-classifier.qza"
+
+diversity:
+    sampling_depth: 30
+
+unassign:
+    unassigner_species_fp: "/home/danielsg/16S_QIIME2/unassign_data/unassigner_species.fasta"
+
+report:
+    study_group_var: "investigator"
+    min_reads: 5
+    richness_subsample_size: 20
+    rmd: "/home/danielsg/16S_QIIME2/scripts/Basic_Bioinformatics_Report.Rmd"
+    R_helper: "/home/danielsg/16S_QIIME2/scripts/helper_functions.R"
+    report_rdata: "/home/danielsg/16S_QIIME2/test/report.RData" # rmd can only have one output so have to put this here
+
+dada2:
+    rscript: "/home/danielsg/16S_QIIME2/scripts/dada2.R"
+    species_training_set: "/home/danielsg/16S_QIIME2/dada2_data/rdp_species_assignment_16.fa.gz"