bio-miga/miga

#!/bin/bash
# Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES, $DATASET
set -e
SCRIPT="stats"
# shellcheck source=scripts/miga.bash
. "$MIGA/scripts/miga.bash" || exit 1
DIR="$PROJECT/data/90.stats"
[[ -d "$DIR" ]] || mkdir -p "$DIR"
cd "$DIR"

# Initialize
miga date > "${DATASET}.start"

# Calculate statistics
for i in raw_reads trimmed_fasta assembly \
         cds essential_genes distances taxonomy ssu ; do
  echo "# $i"
  miga stats --compute-and-save --ignore-empty -P "$PROJECT" -D "$DATASET" -r $i
done

# Finalize
miga date > "${DATASET}.done"
cat <<VERSIONS \
  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
=> MiGA
$(miga --version)
VERSIONS