Pipeline steps to this output (and analysis type):
0	fastq      	: raw data
1	fastp      	: preprocessing
2	filtering  	: preprocessing
3	flash      	: paired-read merging
4	pooling    	: coassembly setup
5	spades     	: assembling
6	prodigal   	: annotation (protein prediction)
7	macsyfinder	: annotation (macromolecular systems, pathways)

Parameters for these steps' outputs:

 ===== 0: fastq (no param) =====

========== 1: fastp ==========
adapter_fasta: null
adapter_sequence: null
adapter_sequence_r2: null
average_qual: 25
chunks: 6
complexity_threshold: 30
compression: 4
correction: false
cpus: 1
cut_front: false
cut_front_mean_quality: 20
cut_front_window_size: 4
cut_mean_quality: 20
cut_right: false
cut_right_mean_quality: 20
cut_right_window_size: 4
cut_tail: false
cut_tail_mean_quality: 20
cut_tail_window_size: 4
cut_window_size: 4
dedup: false
detect_adapter_for_pe: true
disable_adapter_trimming: false
disable_length_filtering: false
disable_quality_filtering: false
disable_trim_poly_g: false
dont_eval_duplication: false
dont_overwrite: false
dup_calc_accuracy: 0
env: null
filter_by_index_threshold: 0
length_limit: 0
length_required: 15
low_complexity_filter: false
machine: saga
max_len1: 0
max_len2: 0
mem: 10
mem_dim: gb
n_base_limit: 5
nodes: 1
overlap_diff_limit: 5
overlap_len_require: 30
overrepresentation_analysis: false
overrepresentation_sampling: 20
partition: null
phred64: false
poly_g_min_len: 10
poly_x_min_len: 10
qualified_quality_phred: 15
reads_to_process: 0
scratch: 10
skip_samples:
- null
split: 0
split_by_lines: false
split_prefix_digits: 4.0
time: 24
trim_front1: 0
trim_front2: 0
trim_poly_g: true
trim_poly_x: false
trim_tail1: 0
trim_tail2: 0
unqualified_percent_limit: 40
verbose: false


========== 2: filtering ==========
chunks: null
cpus: 1
databases:
  H_sapiens: /cluster/projects/nn8075k/03_databases/references/H_sapiens_hg19/hg19
env: null
machine: saga
mem: 30
mem_dim: gb
nodes: 1
partition: null
scratch: scratch
time: 24


========== 3: flash ==========
chunks: 6
cpus: 1
env: null
machine: saga
max_overlap: 90
mem: 2
mem_dim: gb
min_overlap: 10
mismatch: 0
nodes: 1
partition: null
scratch: userscratch
skip_samples:
- null
time: 12


========== 4: pooling ==========
chunks: null
cpus: 1
env: null
machine: saga
mem: 10
mem_dim: gb
nodes: 1
partition: null
pool_single_and_merged: true
scratch: scratch
skip_samples:
- null
time: 24


========== 5: spades ==========
careful: false
checkpoints: all
chunks: 2
continue: true
cov_cutoff: 'off'
cpus: 16
disable_gzip_output: false
disable_rr: false
env: null
hybrid:
- illumina
- nanopore
- pacbio
k:
- '33'
- '55'
- '77'
- '99'
- '127'
machine: saga
mem: 200
mem_dim: gb
meta: true
nodes: 1
only_assembler: true
only_error_correction: false
partition: bigmem
scratch: scratch
skip_samples:
- null
time: 72


========== 6: prodigal ==========
c: false
chunks: null
cpus: 1
env: metagenomics
f: gff
m: false
machine: saga
mem: 20
mem_dim: gb
n: false
nodes: 1
p: meta
partition: null
q: false
scratch: userscratch
skip_samples:
- null
time: 48


========== 7: macsyfinder ==========
accessory_weight: 0.5
chunks: 4
coverage_profile: 0.5
cpus: 10
e_value_search: 0.1
env: macsyfinder
exchangeable_weight: 0.8
i_evalue_sel: 0.001
machine: saga
mandatory_weight: 1.0
mem: 5
mem_dim: gb
models:
- CasFinder
- CONJScan_plasmids
- TFFscan
- TFF-SF
- TXSScan
nodes: 1
out_of_cluster: 0.7
partition: null
redundancy_penalty: 1.5
scratch: scratch
skip_samples:
- null
time: 100